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Sample records for actinobacterial suborder micrococcineae

  1. Kineosphaera nakaumiensis sp. nov., a novel actinobacterial species of the genus Kineosphaera isolated from sediments in Lake Nakaumi.

    PubMed

    Yamada, Chihaya; Matsuo, Yoshihide; Kasai, Hiroaki; Yokota, Akira; Yoon, Jaewoo

    2013-01-01

    A novel actinobacterial strain, designated YM16-381(T), was isolated from sediments of Lake Nakaumi in Shimane Prefecture, Japan. The cell of the strain was motile, non-spore-forming and Gram-positive. The colony was gray-pink and circular on marine agar 2216 medium. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belongs to the family Dermatophilaceae of the suborder Micrococcineae. The highest sequence similarity value of the isolate was 96.2% against Kineosphaera limosa. The diaminopimelic acid in the cell wall was meso-A2pm. The major menaquinone was MK-8(H4). The DNA G+C contents were 70.5 mol%. The major cellular fatty acids were C17:1ω8c, C16:0, C15:0 and C18:1ω9c. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and ninhydrin-positive phosphoglycolipid. On the basis of polyphasic taxonomic studies, strain YM16-381(T) represents a novel species of the genus Kineosphaera within the family Dermatophilaceae, for which the name Kineosphaera nakaumiensis sp. nov. is proposed. The type strain is YM16-381(T) (=KCTC 29138(T)=NBRC 109121(T)).

  2. Actinobacterial community dynamics in long term managed grasslands.

    PubMed

    Jenkins, Sasha N; Waite, Ian S; Blackburn, Adrian; Husband, Rebecca; Rushton, Steven P; Manning, David C; O'Donnell, Anthony G

    2009-05-01

    Palace Leas, a long-term experiment at Cockle Park Farm, Northumberland, UK was established in winter 1896-1897 since when the 13 plots have received regular and virtually unchanged mineral fertiliser and farm yard manure inputs. Fertilisers have had a profound impact on soil pH with the organically fertilised plots showing a significantly higher pH than those receiving mineral fertiliser where ammonium sulphate has led to soil acidification. Here, we investigate the impact of organic and mineral fertilisers on the actinobacterial community structure of these soils using terminal restriction fragment length polymorphism (T-RFLP) and 16S rRNA gene analysis. To differentiate fertiliser effects from seasonal variation, soils were sampled three times over one growing season between May and September 2004 and January 2005. Community profiles obtained using T-RFLP were analysed using multivariate statistics to investigate the relationship between community structure, seasonality and fertiliser management. Soil pH was shown to be the most significant edaphic factor influencing actinobacterial communities. Canonical correspondence analysis, used to investigate the relationship between the 16S rRNA gene community profiles and the environmental parameters, showed that actinobacterial communities also responded to soil water content with major changes evident over the summer months between May and September. Quantitative PCR of the actinobacterial and fungal 16S and 18S rRNA genes, respectively suggested that fungal rRNA gene copy numbers were negatively correlated (P = 0.0131) with increasing actinobacterial signals. A similar relationship (P = 0.000365) was also evident when fatty acid methyl esters indicative of actinobacterial biomass (10-methyloctadecanoic acid) were compared with the amounts of fungal octadecadienoic acid (18:2omega9,12). These results show clearly that soil pH is a major driver of change in actinobacterial communities and that genera such as

  3. Actinobacterial Diversity in the Sediments of Five Cold Springs on the Qinghai-Tibet Plateau

    PubMed Central

    Yang, Jian; Li, Xiaoyan; Huang, Liuqin; Jiang, Hongchen

    2015-01-01

    The actinobacterial diversity was investigated in the sediments of five cold springs in Wuli region on the Qinghai-Tibet Plateau using 16S rRNA gene phylogenetic analysis. The actinobacterial communities of the studied cold springs were diverse and the obtained actinobacterial operational taxonomic units were classified into 12 actinobacterial orders (e.g., Acidimicrobiales, Corynebacteriales, Gaiellales, Geodermatophilales, Jiangellales, Kineosporiales, Micromonosporales, Micrococcales, Nakamurellales, Propionibacteriales, Pseudonocardiales, Streptomycetales) and unclassified Actinobacteria. The actinobacterial composition varied among the investigated cold springs and were significantly correlated (r = 0.748, P = 0.021) to environmental variables. The actinobacterial communities in the cold springs were more diverse than other cold habitats on the Tibetan Plateau, and their compositions showed unique geographical distribution characteristics. Statistical analyses showed that biogeographical isolation and unique environmental conditions might be major factors influencing actinobacterial distribution among the investigated cold springs. PMID:26648925

  4. Reassessment of the Systematics of the Suborder Pseudonocardineae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The suborder Pseudonocardineae proposed by Stackebrandt et al. in 1999 contained only a single family, Pseudonocardineae Embley et al. 1988. Labeda and Kroppenstedt [2000] proposed, on the basis of phylogenetic analysis of a subset of all taxa within the family, that some of the genera be placed in...

  5. Actinobacterial melanins: current status and perspective for the future.

    PubMed

    Manivasagan, Panchanathan; Venkatesan, Jayachandran; Sivakumar, Kannan; Kim, Se-Kwon

    2013-10-01

    Melanins are enigmatic pigments that are produced by a wide variety of microorganisms including several species of bacteria and fungi. Melanins are biological macromolecules with multiple important functions, yet their structures are not well understood. Melanins are frequently used in medicine, pharmacology, and cosmetics preparations. Melanins also have great application potential in agriculture industry. They have several biological functions including photoprotection, thermoregulation, action as free radical sinks, cation chelators, and antibiotics. Plants and insects incorporate melanins as cell wall and cuticle strengtheners, respectively. Actinobacteria are the most economically as well as biotechnologically valuable prokaryotes. However, the melanin properties are, in general, poorly understood. In this review an evaluation is made on the present state of research on actinobacterial melanins and its perspectives. The highlights include the production and biotechnological applications of melanins in agriculture, food, cosmetic and medicinal fields. With increasing advancement in science and technology, there would be greater demands in the future for melanins produced by actinobacteria from various sources.

  6. Complete genome sequence of Sanguibacter keddieii type strain (ST-74T)

    SciTech Connect

    Ivanova, Natalia; Sikorski, Johannes; Sims, David; Brettin, Thomas; Detter, John C.; Han, Cliff; Lapidus, Alla; Copeland, Alex; Glavina Del Rio, Tijana; Nolan, Matt; Chen, Feng; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Pati, Amrita; Mavromatis, Konstantinos; Chen, Amy; Palaniappan, Krishna; D'haeseleer, Patrik; Chain, Patrick; Bristow, Jim; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Goker, Markus; Pukall, Rudiger; Klenk, Hans-Peter; Kyrpides, Nikos

    2009-05-20

    Sanguibacter keddieii is the type species of the genus Sanguibacter, the only described genus within the family of Sanguibacteraceae. Phylogenetically, this family is located in the neighbourhood of the genus Oerskovia and the family Cellulomonadaceae within the actinobacterial suborder Micrococcineae. The strain described in this report was isolated from blood of apparently healthy cows. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the family Sanguibacteraceae, and the 4,253,413 bp long single replicon genome with its 3735 protein-coding and 70 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  7. Marine actinobacterial metabolites: current status and future perspectives.

    PubMed

    Manivasagan, Panchanathan; Venkatesan, Jayachandran; Sivakumar, Kannan; Kim, Se-Kwon

    2013-07-19

    Marine actinobacteriology is one of the major emerging areas of research in tropics. Marine actinobacteria are the most economically as well as biotechnologically valuable prokaryotes. Many representatives of the order Actinomycetales are prolific producers of thousands of biologically active secondary metabolites. Among the actinobacteria, streptomycetes group are considered economically important because out of the approximately more than 10,000 known antibiotics, 50-55% are produced by this genus. The ecological role of actinobacteria in the marine ecosystem is largely neglected and various assumptions meant there was little incentive to isolate marine strains for search and discovery of new drugs. The search for and discovery of novel actinobacteria are of significant interest to drug discovery due to a growing need for the development of new and potent therapeutic agents. In this review an evaluation is made on the present state of research on marine actinobacterial metabolites and its perspectives. The highlights include the production and biotechnological applications of metabolites such as antibiotics, anticancer compounds, melanins, enzymes and enzyme inhibitors, single cell protein and as probiotics in aquaculture. With increasing advancement in science and technology, there would be greater demands in future for new bioactive compounds synthesized by actinobacteria from various marine sources.

  8. A guide to successful bioprospecting: informed by actinobacterial systematics.

    PubMed

    Goodfellow, Michael; Fiedler, Hans-Peter

    2010-08-01

    New structurally diverse natural products are discovered when novel screening procedures are introduced or when high quality biological materials from new sources are examined in existing screens, hence it is important to foster these two aspects of novelty in drug discovery programmes. Amongst prokaryotes, actinomycetes, notably streptomycetes, remain a rich source of new natural products though it has become increasingly difficult to find such metabolites from common actinomycetes as screening 'old friends' leads to the costly rediscovery of known compounds. The bioprospecting strategy which is the subject of this review is based upon the premise that new secondary metabolites can be found by screening relatively small numbers of dereplicated, novel actinomycetes isolated from marine sediments. The success of the strategy is exemplified by the discovery of a range of novel bioactive compounds, notably atrop-abyssomicin C and proximicins A, B and C from Verrucosispora strains isolated from sediment samples taken from the Sea of Japan and the Raune Fjord, respectively, and the dermacozines derived from Dermacoccus strains isolated from the Challenger Deep of the Mariana Trench in the Pacific Ocean. The importance of current advances in prokaryotic systematics in work of this nature is stressed and a plea made that resources be sought to train, support and employ the next generation of actinobacterial systematists.

  9. Actinobacterial Diversity in Volcanic Caves and Associated Geomicrobiological Interactions

    PubMed Central

    Riquelme, Cristina; Marshall Hathaway, Jennifer J.; Enes Dapkevicius, Maria de L. N.; Miller, Ana Z.; Kooser, Ara; Northup, Diana E.; Jurado, Valme; Fernandez, Octavio; Saiz-Jimenez, Cesareo; Cheeptham, Naowarat

    2015-01-01

    volcanic caves are still very limited. To rectify this deficiency, the results from our study help fill in the gaps in our knowledge of actinobacterial diversity and their potential roles in the volcanic cave ecosystems. PMID:26696966

  10. Sponge-associated actinobacterial diversity: validation of the methods of actinobacterial DNA extraction and optimization of 16S rRNA gene amplification.

    PubMed

    Yang, Qi; Franco, Christopher M M; Zhang, Wei

    2015-10-01

    Experiments were designed to validate the two common DNA extraction protocols (CTAB-based method and DNeasy Blood & Tissue Kit) used to effectively recover actinobacterial DNA from sponge samples in order to study the sponge-associated actinobacterial diversity. This was done by artificially spiking sponge samples with actinobacteria (spores, mycelia and a combination of the two). Our results demonstrated that both DNA extraction methods were effective in obtaining DNA from the sponge samples as well as the sponge samples spiked with different amounts of actinobacteria. However, it was noted that in the presence of the sponge, the bacterial 16S rRNA gene could not be amplified unless the combined DNA template was diluted. To test the hypothesis that the extracted sponge DNA contained inhibitors, dilutions of the DNA extracts were tested for six sponge species representing five orders. The results suggested that the inhibitors were co-extracted with the sponge DNA, and a high dilution of this DNA was required for the successful PCR amplification for most of the samples. The optimized PCR conditions, including primer selection, PCR reaction system and program optimization, further improved the PCR performance. However, no single PCR condition was found to be suitable for the diverse sponge samples using various primer sets. These results highlight for the first time that the DNA extraction methods used are effective in obtaining actinobacterial DNA and that the presence of inhibitors in the sponge DNA requires high dilution coupled with fine tuning of the PCR conditions to achieve success in the study of sponge-associated actinobacterial diversity.

  11. Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10T)

    SciTech Connect

    Lapidus, Alla; Pukall, Rudiger; LaButti, Kurt; Copeland, Alex; Glavina Del Rio, Tijana; Nolan, Matt; Chen, Feng; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Rohde, Manfred; Goker, Markus; Pati, Amrita; Ivanova, Natalia; Mavrommatis, Konstantinos; Chen, Amy; Palaniappan, Krishna; D'haeseleer, Patrik; Chain, Patrick; Bristow, Jim; Eisen, Johnathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter

    2009-05-20

    Brachybacterium faecium Collins et al. 1988 is the type species of the genus, and is of phylogenetic interest because of its location in the Dermabacteraceae, a rather isolated family within the actinobacterial suborder Micrococcineae. B. faecium is known for its rod-coccus growth cycle and the ability to degrade uric acid. It grows aerobically or weakly anaerobically. The strain described in this report is a free-living, nonmotile, Gram-positive bacterium, originally isolated from poultry deep litter. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the actinobacterial family Dermabacteraceae, and the 3,614,992 bp long single replicon genome with its 3129 protein-coding and 69 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  12. Fragmented mitochondrial genomes in two suborders of parasitic lice of eutherian mammals (Anoplura and Rhynchophthirina, Insecta)

    PubMed Central

    Shao, Renfu; Barker, Stephen C; Li, Hu; Song, Simon; Poudel, Shreekanta; Su, Yuan

    2015-01-01

    Parasitic lice (order Phthiraptera) infest birds and mammals. The typical animal mitochondrial (mt) genome organization, which consists of a single chromosome with 37 genes, was found in chewing lice in the suborders Amblycera and Ischnocera. The sucking lice (suborder Anoplura) known, however, have fragmented mt genomes with 9–20 minichromosomes. We sequenced the mt genome of the elephant louse, Haematomyzus elephantis – the first species of chewing lice investigated from the suborder Rhynchophthirina. We identified 33 mt genes in the elephant louse, which were on 10 minichromosomes. Each minichromosome is 3.5–4.2 kb in size and has 2–6 genes. Phylogenetic analyses of mt genome sequences confirm that the elephant louse is more closely related to sucking lice than to the chewing lice in the Amblycera and Ischnocera. Our results indicate that mt genome fragmentation is shared by the suborders Anoplura and Rhynchophthirina. Nine of the 10 mt minichromosomes of the elephant louse differ from those of the sucking lice (Anoplura) known in gene content and gene arrangement, indicating that distinct mt karyotypes have evolved in Anoplura and Rhynchophthirina since they diverged ~92 million years ago. PMID:26617060

  13. Fragmented mitochondrial genomes in two suborders of parasitic lice of eutherian mammals (Anoplura and Rhynchophthirina, Insecta).

    PubMed

    Shao, Renfu; Barker, Stephen C; Li, Hu; Song, Simon; Poudel, Shreekanta; Su, Yuan

    2015-11-30

    Parasitic lice (order Phthiraptera) infest birds and mammals. The typical animal mitochondrial (mt) genome organization, which consists of a single chromosome with 37 genes, was found in chewing lice in the suborders Amblycera and Ischnocera. The sucking lice (suborder Anoplura) known, however, have fragmented mt genomes with 9-20 minichromosomes. We sequenced the mt genome of the elephant louse, Haematomyzus elephantis - the first species of chewing lice investigated from the suborder Rhynchophthirina. We identified 33 mt genes in the elephant louse, which were on 10 minichromosomes. Each minichromosome is 3.5-4.2 kb in size and has 2-6 genes. Phylogenetic analyses of mt genome sequences confirm that the elephant louse is more closely related to sucking lice than to the chewing lice in the Amblycera and Ischnocera. Our results indicate that mt genome fragmentation is shared by the suborders Anoplura and Rhynchophthirina. Nine of the 10 mt minichromosomes of the elephant louse differ from those of the sucking lice (Anoplura) known in gene content and gene arrangement, indicating that distinct mt karyotypes have evolved in Anoplura and Rhynchophthirina since they diverged ~92 million years ago.

  14. Developmental biology of Streptomyces from the perspective of 100 actinobacterial genome sequences

    PubMed Central

    Chandra, Govind; Chater, Keith F

    2014-01-01

    To illuminate the evolution and mechanisms of actinobacterial complexity, we evaluate the distribution and origins of known Streptomyces developmental genes and the developmental significance of actinobacteria-specific genes. As an aid, we developed the Actinoblast database of reciprocal blastp best hits between the Streptomyces coelicolor genome and more than 100 other actinobacterial genomes (http://streptomyces.org.uk/actinoblast/). We suggest that the emergence of morphological complexity was underpinned by special features of early actinobacteria, such as polar growth and the coupled participation of regulatory Wbl proteins and the redox-protecting thiol mycothiol in transducing a transient nitric oxide signal generated during physiologically stressful growth transitions. It seems that some cell growth and division proteins of early actinobacteria have acquired greater importance for sporulation of complex actinobacteria than for mycelial growth, in which septa are infrequent and not associated with complete cell separation. The acquisition of extracellular proteins with structural roles, a highly regulated extracellular protease cascade, and additional regulatory genes allowed early actinobacterial stationary phase processes to be redeployed in the emergence of aerial hyphae from mycelial mats and in the formation of spore chains. These extracellular proteins may have contributed to speciation. Simpler members of morphologically diverse clades have lost some developmental genes. PMID:24164321

  15. [The System of the Suborder Zoarcoidei (Pisces, Perciformes) as Inferred from Molecular Genetic Data].

    PubMed

    Radchenko, O A

    2015-11-01

    Based on an analysis of sequence variation in mitochondrial and nuclear markers, the levels of divergence, relationships, and system of the suborder Zoarcoidei was defined. It was demonstrated that DNA lineages of the families Bathymasteridae and Cebidichthyidae were positioned at the bottom ofthe suborder phylogenetic tree. The family Zoarcidae is a monophyletic group, the youngest in the evolutionary terms. Zoarcidae, Anarhichadidae, Neozorcidae, and Eulophiidae form a group of related families. The family Stichaeidae is heterogeneous and has a polyphyletic origin; within this family, the subfamilies Chirolophinae, Alectgiinae, Xiphisterinae, and Stichaeinae are sister taxa. The subfamilies Opisthocentrinae and Lumpeninae are isolated from Stichaedae; Opisthocentrinae is closely associated with the families Pholidae and Ptilichthyidae, and Lumpeninae is closely associated with Zaproridae and Cryptacanthodidae. It is suggested that the rank of subfamilies Opisthocentrinae and Lumpeninae should be raised.

  16. Effect of microbial inoculants on the indigenous actinobacterial endophyte population in the roots of wheat as determined by terminal restriction fragment length polymorphism.

    PubMed

    Conn, Vanessa M; Franco, Christopher M M

    2004-11-01

    The effect of single actinobacterial endophyte seed inoculants and a mixed microbial soil inoculant on the indigenous endophytic actinobacterial population in wheat roots was investigated by using the molecular technique terminal restriction fragment length polymorphism (T-RFLP). Wheat was cultivated either from seeds coated with the spores of single pure actinobacterial endophytes of Microbispora sp. strain EN2, Streptomyces sp. strain EN27, and Nocardioides albus EN46 or from untreated seeds sown in soil with and without a commercial mixed microbial soil inoculant. The endophytic actinobacterial population within the roots of 6-week-old wheat plants was assessed by T-RFLP. Colonization of the wheat roots by the inoculated actinobacterial endophytes was detected by T-RFLP, as were 28 to 42 indigenous actinobacterial genera present in the inoculated and uninoculated plants. The presence of the commercial mixed inoculant in the soil reduced the endophytic actinobacterial diversity from 40 genera to 21 genera and reduced the detectable root colonization by approximately half. The results indicate that the addition of a nonadapted microbial inoculum to the soil disrupted the natural actinobacterial endophyte population, reducing diversity and colonization levels. This was in contrast to the addition of a single actinobacterial endophyte to the wheat plant, where the increase in colonization level could be confirmed even though the indigenous endophyte population was not adversely affected.

  17. Mining Genomes of Three Marine Sponge-Associated Actinobacterial Isolates for Secondary Metabolism

    PubMed Central

    Horn, Hannes; Hentschel, Ute

    2015-01-01

    Here, we report the draft genome sequences of three actinobacterial isolates, Micromonospora sp. RV43, Rubrobacter sp. RV113, and Nocardiopsis sp. RV163 that had previously been isolated from Mediterranean sponges. The draft genomes were analyzed for the presence of gene clusters indicative of secondary metabolism using antiSMASH 3.0 and NapDos pipelines. Our findings demonstrated the chemical richness of sponge-associated actinomycetes and the efficacy of genome mining in exploring the genomic potential of sponge-derived actinomycetes. PMID:26430030

  18. The cell aggregating propensity of probiotic actinobacterial isolates: isolation and characterization of the aggregation inducing peptide pheromone.

    PubMed

    Muthu Selvam, Ramu; Vinothini, Gopal; Palliyarai Thaiyammal, Sethuramalingam; Latha, Selvanathan; Chinnathambi, Arunachalam; Dhanasekaran, Dharumadurai; Padmanabhan, Parasuraman; Ali Alharbi, Sulaiman; Archunan, Govindaraju

    2016-01-01

    The auto-aggregating ability of a probiotic is a prerequisite for colonization and protection of the gastrointestinal tract, whereas co-aggregation provides a close interaction with pathogenic bacteria. Peptide pheromone mediated signaling has been studied in several systems. However, it has not yet been explored in prokaryotes, especially actinobacteria. Hence, in the present study, the diffusible aggregation promoting factor was purified from the culture supernatant of a potent actinobacterial probiont and characterized using 20 different actinobacterial cultures isolated from the gut region of chicken and goat. The results showed that the pheromone-like compound induces the aggregation propensity of treated isolates. The factor was found to be a heat stable, acidic pH resistant, low molecular weight peptide which enhances the biofilm forming ability of other actinobacterial isolates. The aggregation promoting factor represents a bacterial sex factor (pheromone) and its characterization confirms its usage in the probiotic formulation.

  19. Catalogue of genera and their type species in the mite Suborder Uropodina (Acari: Mesostigmata).

    PubMed

    Halliday, R B

    2015-06-11

    This paper provides details of 300 genus-group names in the suborder Uropodina, including the superfamilies Microgynioidea, Thinozerconoidea, Uropodoidea, and Diarthrophalloidea. For each name, the information provided includes a reference to the original description of the genus, the type species and its method of designation, and details of nomenclatural and taxonomic anomalies where necessary. Twenty of these names are excluded from use because they are nomina nuda, junior homonyms, or objective junior synonyms. The remaining 280 available names appear to include a very high level of subjective synonymy, which will need to be resolved in a future comprehensive revision of the Uropodina.

  20. Actinobacterial diversity in limestone deposit sites in Hundung, Manipur (India) and their antimicrobial activities.

    PubMed

    Nimaichand, Salam; Devi, Asem Mipeshwaree; Tamreihao, K; Ningthoujam, Debananda S; Li, Wen-Jun

    2015-01-01

    Studies on actinobacterial diversity in limestone habitats are scarce. This paper reports profiling of actinobacteria isolated from Hundung limestone samples in Manipur, India using ARDRA as the molecular tool for preliminary classification. A total of 137 actinobacteria were clustered into 31 phylotypic groups based on the ARDRA pattern generated and representative of each group was subjected to 16S rRNA gene sequencing. Generic diversity of the limestone isolates consisted of Streptomyces (15 phylotypic groups), Micromonospora (4), Amycolatopsis (3), Arthrobacter (3), Kitasatospora (2), Janibacter (1), Nocardia (1), Pseudonocardia (1) and Rhodococcus (1). Considering the antimicrobial potential of these actinobacteria, 19 showed antimicrobial activities against at least one of the bacterial and candidal test pathogens, while 45 exhibit biocontrol activities against at least one of the rice fungal pathogens. Out of the 137 actinobacterial isolates, 118 were found to have at least one of the three biosynthetic gene clusters (PKS-I, PKS-II, NRPS). The results indicate that 86% of the strains isolated from Hundung limestone deposit sites possessed biosynthetic gene clusters of which 40% exhibited antimicrobial activities. It can, therefore, be concluded that limestone habitat is a promising source for search of novel secondary metabolites.

  1. Diversity and distribution of the bioactive actinobacterial genus Salinispora from sponges along the Great Barrier Reef.

    PubMed

    Vidgen, M E; Hooper, J N A; Fuerst, J A

    2012-03-01

    Isolates from the marine actinobacterial genus Salinispora were cultured from marine sponges collected from along the length of the Great Barrier Reef (GBR), Queensland, Australia. Strains of two species of Salinispora, Salinispora arenicola and "Salinispora pacifica", were isolated from GBR sponges Dercitus xanthus, Cinachyrella australiensis and Hyattella intestinalis. Phylogenetic analysis of the 16S rRNA gene sequences of representative strains, selected via BOX-PCR screening, identified previously unreported phylotypes of the species "S. pacifica". The classification of these microdiverse 16S rRNA groups was further confirmed by analysis of the ribonuclease P RNA (RNase P RNA) gene through both phylogenetic and secondary structure analysis. The use of RNase P RNA sequences combined with 16S rRNA sequences allowed distinction of six new intraspecies phylotypes of "S. pacifica" within the geographical area of the GBR alone. One of these new phylotypes possessed a localised regional distribution within the GBR.

  2. The first troglobitic species of freshwater flatworm of the suborder Continenticola (Platyhelminthes) from South America

    PubMed Central

    de Souza, Stella Teles; Morais, Ana Laura Nunes; Cordeiro, Lívia Medeiros; Leal-Zanchet, Ana Maria

    2015-01-01

    Abstract Brazilian cave diversity, especially of invertebrates, is poorly known. The Bodoquena Plateau, which is located in the Cerrado Biome in central Brazil, has approximately 200 recorded caves with a rich system of subterranean water resources and high troglobitic diversity. Herein we describe a new troglobitic species of Girardia that represents the first obligate cave-dwelling species of the suborder Continenticola in South America. Specimens of the new species, which occur in a limestone cave in the Bodoquena Plateau, in the Cerrado biome, are unpigmented and eyeless. Species recognition in the genus Girardia is difficult, due to their great morphological resemblance. However, the new species can be easily recognized by a unique feature in its copulatory apparatus, namely a large, branched bulbar cavity with multiple diverticula. PMID:25632242

  3. Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122T)

    SciTech Connect

    Land, Miriam; Pukall, Rudiger; Abt, Birte; Goker, Markus; Rohde, Manfred; Glavina Del Rio, Tijana; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavrommatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Hauser, Loren; Chang, Yun-Juan; Jefferies, Cynthia C.; Saunders, Elizabeth; Brettin, Thomas; Detter, John C.; Han, Cliff; Chain, Patrick; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Lapidus, Alla

    2009-05-20

    Beutenbergia cavernae (Groth et al. 1999) is the type species of the genus and is of phylogenetic interest because of its isolated location in the actinobacterial suborder Micrococcineae. B. cavernae HKI 0122T is a Gram-positive, non-motile, non-spore-forming bacterium isolated from a cave in Guangxi (China). B. cavernae grows best under aerobic conditions and shows a rod-coccus growth cycle. Its cell wall peptidoglycan contains the diagnostic L-lysine - L-glutamate interpeptide bridge. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first completed genome sequence from the poorly populated micrococcineal family Beutenbergiaceae, and this 4,669,183 bp long single replicon genome with its 4225 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  4. Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122T)

    SciTech Connect

    Land, Miriam L; Pukall, Rudiger; Abt, Birte; Goker, Markus; Rohde, Manfred; Glavina Del Rio, Tijana; Tice, Hope; Copeland, A; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Ivanova, N; Mavromatis, K; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Saunders, Elizabeth H; Brettin, Tom; Detter, J. Chris; Han, Cliff; Chain, Patrick S. G.; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lapidus, Alla L.

    2009-01-01

    Beutenbergia cavernae (Groth et al. 1999) is the type species of the genus and is of phyloge-netic interest because of its isolated location in the actinobacterial suborder Micrococcineae. B. cavernae HKI 0122T is a Gram-positive, non-motile, non-spore-forming bacterium isolated from a cave in Guangxi (China). B. cavernae grows best under aerobic conditions and shows a rod-coccus growth cycle. Its cell wall peptidoglycan contains the diagnostic L-lysine L-glutamate interpeptide bridge. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first completed genome se-quence from the poorly populated micrococcineal family Beutenbergiaceae, and this 4,669,183 bp long single replicon genome with its 4225 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  5. Structural, functional, and genetic analyses of the actinobacterial transcription factor RbpA.

    PubMed

    Hubin, Elizabeth A; Tabib-Salazar, Aline; Humphrey, Laurence J; Flack, Joshua E; Olinares, Paul Dominic B; Darst, Seth A; Campbell, Elizabeth A; Paget, Mark S

    2015-06-09

    Gene expression is highly regulated at the step of transcription initiation, and transcription activators play a critical role in this process. RbpA, an actinobacterial transcription activator that is essential in Mycobacterium tuberculosis (Mtb), binds selectively to group 1 and certain group 2 σ-factors. To delineate the molecular mechanism of RbpA, we show that the Mtb RbpA σ-interacting domain (SID) and basic linker are sufficient for transcription activation. We also present the crystal structure of the Mtb RbpA-SID in complex with domain 2 of the housekeeping σ-factor, σ(A). The structure explains the basis of σ-selectivity by RbpA, showing that RbpA interacts with conserved regions of σ(A) as well as the nonconserved region (NCR), which is present only in housekeeping σ-factors. Thus, the structure is the first, to our knowledge, to show a protein interacting with the NCR of a σ-factor. We confirm the basis of selectivity and the observed interactions using mutagenesis and functional studies. In addition, the structure allows for a model of the RbpA-SID in the context of a transcription initiation complex. Unexpectedly, the structural modeling suggests that RbpA contacts the promoter DNA, and we present in vivo and in vitro studies supporting this finding. Our combined data lead to a better understanding of the mechanism of RbpA function as a transcription activator.

  6. Actinobacterial diversity across a marine transgression in the deep subsurface off Shimokita Peninsula, Japan

    NASA Astrophysics Data System (ADS)

    Harrison, B. K.; Bailey, J. V.

    2013-12-01

    Sediment horizons represent a significant - but not permanent - barrier to microbial transport. Cells commonly attach to mineral surfaces in unconsolidated sediments. However, by taxis, growth, or passive migration under advecting fluids, some portion of the microbial community may transgress sedimentary boundaries. Few studies have attempted to constrain such transport of community signatures in the marine subsurface and its potential impact on biogeography. Integrated Ocean Drilling Program (IODP) Expedition 337 off the Shimokita Peninsula recovered sediments over a greater than 1km interval representing a gradual decrease of terrestrial influence, from tidal to continental shelf depositional settings. This sequence represents a key opportunity to link subsurface microbial communities to lithological variability and investigate the permanence of community signatures characteristic of distinct depositional regimes. The phylogenetic connectivity between marine and terrestrially-influenced deposits may demonstrate to what degree sediments offer a substantial barrier to cell transport in the subsurface. Previous work has demonstrated that the Actinobacterial phylum is broadly distributed in marine sediments (Maldonado et al., 2005), present and active in the deep subsurface (Orsi et al., 2013), and that marine and terrestrial lineages may potentially be distinguished by 16S rRNA gene sequencing (e.g. Prieto-Davó et al., 2013). We report on Actinobacteria-specific 16S rRNA gene diversity recovered between 1370 and 2642 mbsf with high-throughput sequencing using the Illumina MiSeq platform, as well as selective assembly and analysis of environmental clone libraries.

  7. A novel firmicute protein family related to the actinobacterial resuscitation-promoting factors by non-orthologous domain displacement

    PubMed Central

    Ravagnani, Adriana; Finan, Christopher L; Young, Michael

    2005-01-01

    Background In Micrococcus luteus growth and resuscitation from starvation-induced dormancy is controlled by the production of a secreted growth factor. This autocrine resuscitation-promoting factor (Rpf) is the founder member of a family of proteins found throughout and confined to the actinobacteria (high G + C Gram-positive bacteria). The aim of this work was to search for and characterise a cognate gene family in the firmicutes (low G + C Gram-positive bacteria) and obtain information about how they may control bacterial growth and resuscitation. Results In silico analysis of the accessory domains of the Rpf proteins permitted their classification into several subfamilies. The RpfB subfamily is related to a group of firmicute proteins of unknown function, represented by YabE of Bacillus subtilis. The actinobacterial RpfB and firmicute YabE proteins have very similar domain structures and genomic contexts, except that in YabE, the actinobacterial Rpf domain is replaced by another domain, which we have called Sps. Although totally unrelated in both sequence and secondary structure, the Rpf and Sps domains fulfil the same function. We propose that these proteins have undergone "non-orthologous domain displacement", a phenomenon akin to "non-orthologous gene displacement" that has been described previously. Proteins containing the Sps domain are widely distributed throughout the firmicutes and they too fall into a number of distinct subfamilies. Comparative analysis of the accessory domains in the Rpf and Sps proteins, together with their weak similarity to lytic transglycosylases, provide clear evidence that they are muralytic enzymes. Conclusions The results indicate that the firmicute Sps proteins and the actinobacterial Rpf proteins are cognate and that they control bacterial culturability via enzymatic modification of the bacterial cell envelope. PMID:15774001

  8. In vitro probiotic profile based selection of indigenous actinobacterial probiont Streptomyces sp. JD9 for enhanced broiler production.

    PubMed

    Latha, Selvanathan; Vinothini, Gopal; John Dickson Calvin, Devadasan; Dhanasekaran, Dharumadurai

    2016-01-01

    The present study was undertaken to select exclusive indigenous actinobacterial probiont for broiler health improvement based on in vitro probiotic potentials. In total, 18 actinobacterial cultures isolated from chicken were screened for survivability (resistance to low pH, pepsin, bile and pancreatin), colonization (auto-aggregation, hydrophobicity and co-aggregation) and safety (antibiotic susceptibility and non-haemolytic activity). Ten cultures showed excellent viability at pH 2 and most of the acid-tolerant isolates exhibited resistance to pepsin (3 mg/mL), bile (0.3%) and pancreatin (1 mg/mL). Besides, the examined isolates displayed efficient adhesion properties. All the isolates were susceptible to 9 different antibiotics and none of them exhibited β-haemolytic activity. Moreover, the culture JD9 revealed remarkable probiotic features compared to the other isolates, which was identified as Streptomyces sp. JD9 (KF878075). Taken together, the present study suggests that the probiont Streptomyces sp. JD9 could potentially be used in broiler practices as a feed additive to facilitate enhanced broiler production.

  9. Dwarf males of Octolasmis warwickii (Cirripedia: Thoracica): the first example of coexistence of males and hermaphrodites in the suborder Lepadomorpha.

    PubMed

    Yusa, Yoichi; Takemura, Mayuko; Miyazaki, Katsumi; Watanabe, Tetsuya; Yamato, Shigeyuki

    2010-06-01

    In the lepadomorph barnacle Octolasmis warwickii, individuals are often found attached to the scutum of conspecifics living externally on the crab hosts. To test whether these conspecific-attached individuals are dwarf males, as are known to occur in other suborders of barnacles, we compared the pattern of attachment, size-frequency distribution, and reproductive status of the conspecific-attached (Con-A) and crab-attached (Crab-A) individuals. Con-As were smaller than Crab-As. There was a positive relationship between the body size of Crab-As and the number of individuals on them. Con-As had longer penises than Crab-As of the same body size, and their testes were better developed. The four largest Con-As examined were brooding eggs. These results indicate that Con-As of O. warwickii are dwarf males, with a potential to become hermaphroditic. This represents the first known example of coexistence of males and hermaphrodites in the suborder Lepadomorpha. The mating group size of O. warwickii was smaller than in its hermaphroditic congeners but larger than in barnacles with dwarf males and females, which supports the current theories that group size is important for the evolution of sexuality patterns in barnacles.

  10. Marine-derived myxobacteria of the suborder Nannocystineae: An underexplored source of structurally intriguing and biologically active metabolites

    PubMed Central

    Schäberle, Till F

    2016-01-01

    Summary Myxobacteria are famous for their ability to produce most intriguing secondary metabolites. Till recently, only terrestrial myxobacteria were in the focus of research. In this review, however, we discuss marine-derived myxobacteria, which are particularly interesting due to their relatively recent discovery and due to the fact that their very existence was called into question. The to-date-explored members of these halophilic or halotolerant myxobacteria are all grouped into the suborder Nannocystineae. Few of them were chemically investigated revealing around 11 structural types belonging to the polyketide, non-ribosomal peptide, hybrids thereof or terpenoid class of secondary metabolites. A most unusual structural type is represented by salimabromide from Enhygromyxa salina. In silico analyses were carried out on the available genome sequences of four bacterial members of the Nannocystineae, revealing the biosynthetic potential of these bacteria. PMID:27340488

  11. Complete genome sequence of the soil actinomycete Kocuria rhizophila.

    PubMed

    Takarada, Hiromi; Sekine, Mitsuo; Kosugi, Hiroki; Matsuo, Yasunori; Fujisawa, Takatomo; Omata, Seiha; Kishi, Emi; Shimizu, Ai; Tsukatani, Naofumi; Tanikawa, Satoshi; Fujita, Nobuyuki; Harayama, Shigeaki

    2008-06-01

    The soil actinomycete Kocuria rhizophila belongs to the suborder Micrococcineae, a divergent bacterial group for which only a limited amount of genomic information is currently available. K. rhizophila is also important in industrial applications; e.g., it is commonly used as a standard quality control strain for antimicrobial susceptibility testing. Sequencing and annotation of the genome of K. rhizophila DC2201 (NBRC 103217) revealed a single circular chromosome (2,697,540 bp; G+C content of 71.16%) containing 2,357 predicted protein-coding genes. Most of the predicted proteins (87.7%) were orthologous to actinobacterial proteins, and the genome showed fairly good conservation of synteny with taxonomically related actinobacterial genomes. On the other hand, the genome seems to encode much smaller numbers of proteins necessary for secondary metabolism (one each of nonribosomal peptide synthetase and type III polyketide synthase), transcriptional regulation, and lateral gene transfer, reflecting the small genome size. The presence of probable metabolic pathways for the transformation of phenolic compounds generated from the decomposition of plant materials, and the presence of a large number of genes associated with membrane transport, particularly amino acid transporters and drug efflux pumps, may contribute to the organism's utilization of root exudates, as well as the tolerance to various organic compounds.

  12. Diversity and chemical defense role of culturable non-actinobacterial bacteria isolated from the South China Sea gorgonians.

    PubMed

    Peng, Jiang; Zhang, Xiaoyong; Xu, Xinya; He, Fei; Qi, Shuhua

    2013-04-01

    The diversity of culturable non-actinobacterial (NA) bacteria associated with four species of South China Sea gorgonians was investigated using culture-dependent methods followed by analysis of the bacterial 16S rDNA sequence. A total of 76 bacterial isolates were recovered and identified, which belonged to 21 species of 7 genera, and Bacillus was the most diverse genus. Fifty-one percent of the 76 isolates displayed antibacterial activities, and most of them belonged to the Bacillus genus. From the culture broth of gorgonian-associated Bacillus methylotrophicus SCSGAB0092 isolated from gorgonian Melitodes squamata, 11 antimicrobial lipopeptides including seven surfactins and four iturins were obtained. These results imply that Bacillus strains associated with gorgonians play roles in coral defense mechanisms through producing antimicrobial substances. This study, for the first time, compares the diversity of culturable NA bacterial communities among four species of South China Sea gorgonians and investigates the secondary metabolites of gorgonian-associated B. methylotrophicus SCSGAB0092.

  13. Morphological, Physiological, and Taxonomic Characterization of Actinobacterial Isolates Living as Endophytes of Cacao Pods and Cacao Seeds.

    PubMed

    Tchinda, Romaric Armel Mouafo; Boudjeko, Thaddée; Simao-Beaunoir, Anne-Marie; Lerat, Sylvain; Tsala, Éric; Monga, Ernest; Beaulieu, Carole

    2016-01-01

    Vascular plants are commonly colonized by endophytic actinobacteria. However, very little is known about the relationship between these microorganisms and cacao fruits. In order to determine the physiological and taxonomic relationships between the members of this community, actinobacteria were isolated from cacao fruits and seeds. Among the 49 isolates recovered, 11 morphologically distinct isolates were selected for further characterization. Sequencing of the 16S rRNA gene allowed the partition of the selected isolates into three phylogenetic clades. Most of the selected endophytic isolates belonged to the Streptomyces violaceusniger clade. Physiological characterization was carried out and a similarity index was used to cluster the isolates. However, clustering based on physiological properties did not match phylogenetic lineages. Isolates were also characterized for traits commonly associated with plant growth-promoting bacteria, including antibiosis and auxin biosynthesis. All isolates exhibited resistance to geldanamycin, whereas only two isolates were shown to produce this antibiotic. Endophytes were inoculated on radish seedlings and most isolates were found to possess plant growth-promoting abilities. These endophytic actinobacteria inhibited the growth of various plant pathogenic fungi and/or bacteria. The present study showed that S. violaceusniger clade members represent a significant part of the actinobacterial community living as endophytes in cacao fruits and seeds. While several members of this clade are known to be geldanamycin producers and efficient biocontrol agents of plant diseases, we herein established the endophytic lifestyle of some of these microorganisms, demonstrating their potential as plant health agents.

  14. Structure of an Actinobacterial-Type [NiFe]-Hydrogenase Reveals Insight into O2-Tolerant H2 Oxidation.

    PubMed

    Schäfer, Caspar; Bommer, Martin; Hennig, Sandra E; Jeoung, Jae-Hun; Dobbek, Holger; Lenz, Oliver

    2016-02-02

    A novel group of bacterial [NiFe]-hydrogenases is responsible for high-affinity H2 uptake from the troposphere, and is therefore thought to play an important role in the global H2 cycle. Here we present the first crystal structure at 2.85-Å resolution of such an actinobacterial-type hydrogenase (AH), which was isolated from the dihydrogen oxidizing bacterium, Ralstonia eutropha. The enzyme has a dimeric structure carrying two active [NiFe] sites that are interconnected by six [4Fe4S] clusters over a range of approximately 90 Å. Unlike most other [NiFe]-hydrogenases, the [4Fe4S] cluster proximal to the [NiFe] site is coordinated by three cysteines and one aspartate. Mutagenesis experiments revealed that this aspartate residue is related to the apparent O2 insensitivity of the AH. Our data provide first structural insight into specialized hydrogenases that are supposed to consume atmospheric H2 under challenging conditions, i.e. at high O2 concentration and wide temperature and pH ranges.

  15. Morphological, Physiological, and Taxonomic Characterization of Actinobacterial Isolates Living as Endophytes of Cacao Pods and Cacao Seeds

    PubMed Central

    Tchinda, Romaric Armel Mouafo; Boudjeko, Thaddée; Simao-Beaunoir, Anne-Marie; Lerat, Sylvain; Tsala, Éric; Monga, Ernest; Beaulieu, Carole

    2016-01-01

    Vascular plants are commonly colonized by endophytic actinobacteria. However, very little is known about the relationship between these microorganisms and cacao fruits. In order to determine the physiological and taxonomic relationships between the members of this community, actinobacteria were isolated from cacao fruits and seeds. Among the 49 isolates recovered, 11 morphologically distinct isolates were selected for further characterization. Sequencing of the 16S rRNA gene allowed the partition of the selected isolates into three phylogenetic clades. Most of the selected endophytic isolates belonged to the Streptomyces violaceusniger clade. Physiological characterization was carried out and a similarity index was used to cluster the isolates. However, clustering based on physiological properties did not match phylogenetic lineages. Isolates were also characterized for traits commonly associated with plant growth-promoting bacteria, including antibiosis and auxin biosynthesis. All isolates exhibited resistance to geldanamycin, whereas only two isolates were shown to produce this antibiotic. Endophytes were inoculated on radish seedlings and most isolates were found to possess plant growth-promoting abilities. These endophytic actinobacteria inhibited the growth of various plant pathogenic fungi and/or bacteria. The present study showed that S. violaceusniger clade members represent a significant part of the actinobacterial community living as endophytes in cacao fruits and seeds. While several members of this clade are known to be geldanamycin producers and efficient biocontrol agents of plant diseases, we herein established the endophytic lifestyle of some of these microorganisms, demonstrating their potential as plant health agents. PMID:26947442

  16. On some surface structures of potential taxonomic importance in families of the suborders Polydesmidea and Dalodesmidea (Polydesmida, Diplopoda)

    PubMed Central

    Akkari, Nesrine; Enghoff, Henrik

    2011-01-01

    Abstract Surface structures have rarely been the subject of a comprehensive study in Polydesmida despite their tremendous variety within this order. A number of these peripheral structures are here studied in most families of the suborders Polydesmidea and Dalodesmidea (sensu Hoffman 1980), using scanning electron microscopy. An illustrated description of the surface sculpture of the prozonite, the limbus and the intercalary cuticular micro-scutes on the metazonite is given for the first time for the studied families, together with an account of some other poorly known surface structures. Taken together, these characters allow us to recognize two main groupings of families. The families Ammodesmidae, Cryptodesmidae, Cyrtodesmidae, Haplodesmidae, Oniscodesmidae and Pyrgodesmidae have knobs on the posterior part of the prozonites, a toothed to lobed limbus, and no micro-scutes on the metazonites, wheras the families Fuhrmannodesmidae, Polydesmidae, Dalodesmidae, Macrosternodesmidae, Nearctodesmidae, Opisotretidae and Trichopolydesmidae have no knobs on the posterior part of the prozonites, a spiky or reduced limbus, and intercalary micro-scutes on the metazonites. The results are complemented with literature records and compared with current taxonomic and phylogenetic interpretations of the group. PMID:22303092

  17. Tomitella biformata gen. nov., sp. nov., a new member of the suborder Corynebacterineae isolated from a permafrost ice wedge.

    PubMed

    Katayama, Taiki; Kato, Tomoko; Tanaka, Michiko; Douglas, Thomas A; Brouchkov, Anatoli; Abe, Ayumi; Sone, Teruo; Fukuda, Masami; Asano, Kozo

    2010-12-01

    Gram-reaction-positive, aerobic, non-spore-forming, irregular rod-shaped bacteria, designated AHU1821(T) and AHU1820, were isolated from an ice wedge in the Fox permafrost tunnel, Alaska. The strains were psychrophilic, growing at -5 to 27°C. Phylogenetic analysis of the 16S rRNA and gyrB gene sequences indicated that the ice-wedge isolates formed a clade distinct from other mycolic-acid-containing bacteria within the suborder Corynebacterineae. The cell wall of strains AHU1821(T) and AHU1820 contained meso-diaminopimelic acid, arabinose and galactose, indicating chemotype IV. The muramic acids in the peptidoglycan were glycolated. The predominant menaquinone was MK-9(H(2)). The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and an unidentified glycolipid. The major fatty acids were hexadecenoic acid (C(16 : 1)), hexadecanoic acid (C(16 : 0)), octadecenoic acid (C(18 : 1)) and tetradecanoic acid (C(14 : 0)). Tuberculostearic acid was present in relatively small amounts (1 %). Strains AHU1821(T) and AHU1820 contained mycolic acids with 42-52 carbons. The DNA G+C content of the two strains was 69.3-71.6 mol% (T(m)). 16S rRNA, rpoB and recA gene sequences were identical between strains AHU1821(T) and AHU1820 and those of the gyrB gene showed 99.9 % similarity. Based on phylogenetic and phenotypic evidence, strains AHU1821(T) and AHU1820 represent a single novel species of a novel genus, for which the name Tomitella biformata gen. nov., sp. nov. is proposed. The type strain of Tomitella biformata is AHU1821(T) (=DSM 45403(T) =NBRC 106253(T)).

  18. A millipede missing link: Dobrodesmidae, a remarkable new polydesmidan
    millipede family from Brazil with supernumerary rings (Diplopoda, Polydesmida), and the establishment of a new suborder Dobrodesmidea.

    PubMed

    Shear, William A; Ferreira, Rodrigo Lopes; Iniesta, Luiz Felipe Moretti; Marek, Paul

    2016-10-25

    Dobrodesmus mirabilis n. gen., n. sp. is described from a limestone cave in the state of Bahia, Brazil. The new species is unique among millipedes of the order Polydesmida in having 39+t rings in adult males, two rather than four spinnerets, and in its highly plesiomorphic gonopods, which resemble those of basal members of the orders Callipodida and Stemmiulida. The presence of 39 rings is notable because members of the Polydesmida, the most species rich order of millipedes (>5000 spp.) normally stop development at 19+t rings. Because of these characters, D. mirabilis is the basis for the proposal of a new family (Dobrodesmidae) and a new suborder (Dobrodesmidea) of polydesmidans.

  19. Cultural, Transcriptomic, and Proteomic Analyses of Water-Stressed Cells of Actinobacterial Strains Isolated from Compost: Ecological Implications in the Fed-Batch Composting Process

    PubMed Central

    Narihiro, Takashi; Kanosue, Yuji; Hiraishi, Akira

    2016-01-01

    This study was undertaken to examine the effects of water activity (aw) on the viability of actinobacterial isolates from a fed-batch composting (FBC) process by comparing culturability and stainability with 5-cyano-2,3-ditoryl tetrazolium chloride (CTC). The FBC reactor as the source of these bacteria was operated with the daily loading of household biowaste for 70 d. During this period of composting, aw in the reactor decreased linearly with time and reached approximately 0.95 at the end of operation. The plate counts of aerobic chemoorganotrophic bacteria were 3.2-fold higher than CTC-positive (CTC+) counts on average at the fully acclimated stage (after 7 weeks of operation), in which Actinobacteria predominated, as shown by lipoquinone profiling and cultivation methods. When the actinobacterial isolates from the FBC process were grown under aw stress, no significant differences were observed in culturability among the cultures, whereas CTC stainability decreased with reductions in aw levels. A cDNA microarray-based transcriptomic analysis of a representative isolate showed that many of the genes involved in cellular metabolism and genetic information processing were down-regulated by aw stress. This result was fully supported by a proteomic analysis. The results of the present study suggest that, in low aw mature compost, the metabolic activity of the community with Actinobacteria predominating is temporarily reduced to a level that hardly reacts with CTC; however, these bacteria are easily recoverable by exposure to a high aw culture medium. This may be a plausible reason why acclimated FBC reactors in which Actinobacteria predominate yields higher plate counts than CTC+ counts. PMID:27246805

  20. Complete genome sequence of Kytococcus sedentarius type strain (strain 541T)

    SciTech Connect

    Sims, David; Brettin, Thomas; Detter, John C.; Han, Cliff; Lapidus, Alla; Copeland, Alex; Glavina Del Rio, Tijana; Nolan, Matt; Chen, Feng; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ovchinnikova, Galina; Pati, Amrita; Ivanova, Natalia; Mavrommatis, Konstantinos; Chen, Amy; Palaniappan, Krishna; D'haeseleer, Patrick; Chain, Patrick; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Schneider, Susanne; Goker, Markus; Pukall, Rudiger; Kyrpides, Nikos C.; Klenk, Hans-Peter

    2009-05-20

    Kytococcus sedentarius (ZoBell and Upham 1944) Stackebrandt et al. 1995 is the type strain of the species, and is of phylogenetic interest because of its location in the Dermacoccaceae, a poorly studied family within the actinobacterial suborder Micrococcineae. K. sedentarius is known for the production of oligoketide antibiotics as well as for its role as an opportunistic pathogen causing valve endocarditis, hemorrhagic pneumonia, and pitted keratolysis. It is strictly aerobic and can only grow when several amino acids are provided in the medium. The strain described in this report is a free-living, nonmotile, Gram-positive bacterium, originally isolated from a marine environment. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family Dermacoccaceae and the 2,785,024 bp long single replicon genome with its 2639 protein-coding and 64 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  1. [Fauna and distribution of nematodes from the suborders spirurata and filariata parasitizing cattle in Dagestan, from the perspective of vertical zoning].

    PubMed

    Zubairova, M M; Ataev, A M

    2010-01-01

    Cattle of Dagestan are infested with several nematode species from the suborders Spirurata and Filariata, and extensiveness of the invasion depends greatly on the altitude above sea level. Level of infestation with Thelazia rhodesi, Th. gulosa, and Th. skrjabini is 38% in plains, 20% in submontane, and 5% in mountain zone. The same tendency is observed for the species Gongylonema pulchrum--45, 22, and 10%, respectively. Infestation with Setaria labiato-papillosa is 27.3% on average. Infestation with Onchocerca gutturosa and O. lienalis is 11% in plains and 3% in mountain and submontane zones; infestation with Stephanofilaria assamensis and S. stilesi in these zones is 18 and 5%, respectively. In mountain localities situated higher than 1000 m a. s. l. only G. pulchrum is occurred.

  2. The currently used commercial DNA-extraction methods give different results of clostridial and actinobacterial populations derived from human fecal samples.

    PubMed

    Maukonen, Johanna; Simões, Catarina; Saarela, Maria

    2012-03-01

    Recently several human health-related microbiota studies have had partly contradictory results. As some differences may be explained by methodologies applied, we evaluated how different storage conditions and commonly used DNA-extraction kits affect bacterial composition, diversity, and numbers of human fecal microbiota. According to our results, the DNA-extraction did not affect the diversity, composition, or quantity of Bacteroides spp., whereas after a week's storage at -20 °C, the numbers of Bacteroides spp. were 1.6-2.5 log units lower (P < 0.05). Furthermore, the numbers of predominant bacteria, Eubacterium rectale (Erec)-group, Clostridium leptum group, bifidobacteria, and Atopobium group were 0.5-4 log units higher (P < 0.05) after mechanical DNA-extraction as detected with qPCR, regardless of storage. Furthermore, the bacterial composition of Erec-group differed significantly after different DNA-extractions; after enzymatic DNA-extraction, the most prevalent genera detected were Roseburia (39% of clones) and Coprococcus (10%), whereas after mechanical DNA-extraction, the most prevalent genera were Blautia (30%), Coprococcus (13%), and Dorea (10%). According to our results, rigorous mechanical lysis enables detection of higher bacterial numbers and diversity from human fecal samples. As it was shown that the results of clostridial and actinobacterial populations are highly dependent on the DNA-extraction methods applied, the use of different DNA-extraction protocols may explain the contradictory results previously obtained.

  3. Complete mitochondrial genome of Membranipora grandicella (Bryozoa: Cheilostomatida) determined with next-generation sequencing: the first representative of the suborder Malacostegina.

    PubMed

    Shen, Xin; Tian, Mei; Meng, Xueping; Liu, Huilian; Cheng, Hanliang; Zhu, Changbao; Zhao, Fangqing

    2012-09-01

    Next-generation sequencing (NGS) has proven a valuable platform for fast and easy obtaining of large numbers of sequences at relatively low cost. In this study we use shot-gun sequencing method on Illumina HiSeq 2000, to obtain enough sequences for the assembly of the bryozoan Membranipora grandicella (Bryozoa: Cheilostomatida) mitochondrial genome, which is the first representative of the suborder Malacostegina. The complete mitochondrial genome is 15,861 bp in length, which is relatively larger than other studied bryozoans. The mitochondrial genome contains 13 protein-coding genes, 2 ribosomal RNAs and 20 transfer RNAs. To investigate the phylogenetic position and the inner relationships of the phylum Bryozoa, phylogenetic trees were constructed with amino acid sequences of 11 PCGs from 30 metazoans. Two superclades of protostomes, namely Lophotrochozoa and Ecdysozoa, are recovered as monophyletic with strong support in both ML and Bayesian analyses. Somewhat to surprise, Bryozoa appears as the sister group of Chaetognatha with moderate or high support. The relationship among five bryozoans is Tubulipora flabellaris + (M. grandicella + (Flustrellidra hispida + (Bugula neritina + Watersipora subtorquata))), which supports for the view that Cheilostomatida is not a natural, monophyletic clade. NGS proved to be a quick and easy method for sequencing a complete mitochondrial genome.

  4. Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant.

    PubMed

    Persson, Tomas; Battenberg, Kai; Demina, Irina V; Vigil-Stenman, Theoden; Vanden Heuvel, Brian; Pujic, Petar; Facciotti, Marc T; Wilbanks, Elizabeth G; O'Brien, Anna; Fournier, Pascale; Cruz Hernandez, Maria Antonia; Mendoza Herrera, Alberto; Médigue, Claudine; Normand, Philippe; Pawlowski, Katharina; Berry, Alison M

    2015-01-01

    Frankia strains are nitrogen-fixing soil actinobacteria that can form root symbioses with actinorhizal plants. Phylogenetically, symbiotic frankiae can be divided into three clusters, and this division also corresponds to host specificity groups. The strains of cluster II which form symbioses with actinorhizal Rosales and Cucurbitales, thus displaying a broad host range, show suprisingly low genetic diversity and to date can not be cultured. The genome of the first representative of this cluster, Candidatus Frankia datiscae Dg1 (Dg1), a microsymbiont of Datisca glomerata, was recently sequenced. A phylogenetic analysis of 50 different housekeeping genes of Dg1 and three published Frankia genomes showed that cluster II is basal among the symbiotic Frankia clusters. Detailed analysis showed that nodules of D. glomerata, independent of the origin of the inoculum, contain several closely related cluster II Frankia operational taxonomic units. Actinorhizal plants and legumes both belong to the nitrogen-fixing plant clade, and bacterial signaling in both groups involves the common symbiotic pathway also used by arbuscular mycorrhizal fungi. However, so far, no molecules resembling rhizobial Nod factors could be isolated from Frankia cultures. Alone among Frankia genomes available to date, the genome of Dg1 contains the canonical nod genes nodA, nodB and nodC known from rhizobia, and these genes are arranged in two operons which are expressed in D. glomerata nodules. Furthermore, Frankia Dg1 nodC was able to partially complement a Rhizobium leguminosarum A34 nodC::Tn5 mutant. Phylogenetic analysis showed that Dg1 Nod proteins are positioned at the root of both α- and β-rhizobial NodABC proteins. NodA-like acyl transferases were found across the phylum Actinobacteria, but among Proteobacteria only in nodulators. Taken together, our evidence indicates an Actinobacterial origin of rhizobial Nod factors.

  5. Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant

    PubMed Central

    Persson, Tomas; Battenberg, Kai; Demina, Irina V.; Vigil-Stenman, Theoden; Vanden Heuvel, Brian; Pujic, Petar; Facciotti, Marc T.; Wilbanks, Elizabeth G.; O'Brien, Anna; Fournier, Pascale; Cruz Hernandez, Maria Antonia; Mendoza Herrera, Alberto; Médigue, Claudine; Normand, Philippe; Pawlowski, Katharina; Berry, Alison M.

    2015-01-01

    Frankia strains are nitrogen-fixing soil actinobacteria that can form root symbioses with actinorhizal plants. Phylogenetically, symbiotic frankiae can be divided into three clusters, and this division also corresponds to host specificity groups. The strains of cluster II which form symbioses with actinorhizal Rosales and Cucurbitales, thus displaying a broad host range, show suprisingly low genetic diversity and to date can not be cultured. The genome of the first representative of this cluster, Candidatus Frankia datiscae Dg1 (Dg1), a microsymbiont of Datisca glomerata, was recently sequenced. A phylogenetic analysis of 50 different housekeeping genes of Dg1 and three published Frankia genomes showed that cluster II is basal among the symbiotic Frankia clusters. Detailed analysis showed that nodules of D. glomerata, independent of the origin of the inoculum, contain several closely related cluster II Frankia operational taxonomic units. Actinorhizal plants and legumes both belong to the nitrogen-fixing plant clade, and bacterial signaling in both groups involves the common symbiotic pathway also used by arbuscular mycorrhizal fungi. However, so far, no molecules resembling rhizobial Nod factors could be isolated from Frankia cultures. Alone among Frankia genomes available to date, the genome of Dg1 contains the canonical nod genes nodA, nodB and nodC known from rhizobia, and these genes are arranged in two operons which are expressed in D. glomerata nodules. Furthermore, Frankia Dg1 nodC was able to partially complement a Rhizobium leguminosarum A34 nodC::Tn5 mutant. Phylogenetic analysis showed that Dg1 Nod proteins are positioned at the root of both α- and β-rhizobial NodABC proteins. NodA-like acyl transferases were found across the phylum Actinobacteria, but among Proteobacteria only in nodulators. Taken together, our evidence indicates an Actinobacterial origin of rhizobial Nod factors. PMID:26020781

  6. Biomedical potential of actinobacterially synthesized selenium nanoparticles with special reference to anti-biofilm, anti-oxidant, wound healing, cytotoxic and anti-viral activities.

    PubMed

    Ramya, Suseenthar; Shanmugasundaram, Thangavel; Balagurunathan, Ramasamy

    2015-10-01

    Currently, there is an ever-increasing need to develop environmentally benign processes in place of synthetic protocols. As a result, researchers in the field of nanoparticle synthesis are focusing their attention on microbes from rare biological ecosystems. One potential actinobacterium, Streptomyces minutiscleroticus M10A62 isolated from a magnesite mine had the ability to synthesize selenium nanoparticles (SeNPs), extracellularly. Actinobacteria mediated SeNP synthesis were characterized by UV-visible, Fourier transform infrared (FT-IR), X-ray diffraction (XRD), energy dispersive X-ray spectroscopy (EDX) and high resolution transmission electron microscopy (HR-TEM) analysis. The UV-spectral analysis of SeNPs indicated the maximum absorption at 510nm, FT-IR spectral analysis confirms the presence of capping protein, peptide, amine and amide groups. The selenium signals confirm the presence of SeNPs. All the diffraction peaks in the XRD pattern and HR-TEM confirm the size of SeNPs in the range of 10-250nm. Further, the anti-biofilm and antioxidant activity of the SeNPs increased proportionally with rise in concentration, and the test strains reduced to 75% at concentration of 3.2μg. Selenium showed significant anti-proliferative activity against HeLa and HepG2 cell lines. The wound healing activity of SeNPs reveals that 5% selenium oinment heals the excision wound of Wistar rats up to 85% within 18 days compared to the standard ointment. The biosynthesized SeNPs exhibited good antiviral activity against Dengue virus. The present study concludes that extremophilic actinobacterial strain was a novel source for SeNPs with versatile biomedical applications and larger studies are needed to quantify these observed effects of SeNPs.

  7. Genus III. Actinokineospora Hasegawa 1988a, 449vp

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The physiology, systematics and ecology of the species that currently composes the actinobacterial genus Actinokineospora is presented. The phylogenetic position of the species within this genus relative to the other genera within the suborder Pseudonocardineae is discussed. Methods for isolation,...

  8. Order XIII. Pseudonocardineae ord.nov.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The formal description of the actinobacterial higher taxon, the suborder Pseudonocardineae, is presented. The differential morphological and chemotaxonomic characteristics and diagnostic signature nucleotides from the 16S rRNA gene for the families Actinosynnemataceae and Pseudonocardiaceae in the ...

  9. Brain and sense organ anatomy and histology of two species of phyletically basal non-Antarctic thornfishes of the Antarctic suborder Notothenioidei (Perciformes: Bovichtidae).

    PubMed

    Eastman, Joseph T; Lannoo, Michael J

    2007-06-01

    The predominantly non-Antarctic family Bovichtidae is phyletically basal within the perciform suborder Notothenioidei, the dominant component of the Antarctic fish fauna. In this article we focus on the South Atlantic bovichtids Bovichtus diacanthus, the klipfish from tide pools at Tristan da Cunha, and Cottoperca gobio, the frogmouth from the Patagonian shelf and Falkland Islands. We document the anatomy and histology of the brains, olfactory apparatus, retina, and cephalic lateral line system. We also use the microvascular casting agent Microfil to examine ocular vascular structures. We provide detailed drawings of the brains and cranial nerves of both species. Typical of perciforms, the brains of both species have a well-developed tectum and telencephalon and robust thalamic nuclei. The telencephalon of C. gobio is prominently lobed, with the dorsomedial nucleus more conspicuous than in any other notothenioid. The corpus cerebelli is relatively small and upright and, unlike other notothenioids, has prominent transverse sulci on the dorsal and caudal surfaces. Areas for lateral line mechanoreception (eminentia granularis and crista cerebellaris) are also conspicuous but olfactory, gustatory, and somatosensory areas are less prominent. The anterior lateral line nerve complex is larger than the posterior lateral line nerve in B. diacanthus, and in their cephalic lateral line systems both species possess branched membranous tubules (which do not contain neuromasts) with small pores. These are especially complex in B. diacanthus where they become increasingly branched and more highly pored in progressively larger specimens. Superficial neuromasts are sparse. Both species have duplex (cone and rod) retinae that are 1.25-fold thicker and have nearly 5-fold more photoreceptors and than those of most Antarctic notothenioids. Convergence ratios are also high for bovichtids. Bovichtus diacanthus has a yellow intraocular filter in the dorsal aspect of the cornea. Both

  10. Recent Transmission of a Novel Alphacoronavirus, Bat Coronavirus HKU10, from Leschenault's Rousettes to Pomona Leaf-Nosed Bats: First Evidence of Interspecies Transmission of Coronavirus between Bats of Different Suborders

    PubMed Central

    Lau, Susanna K. P.; Li, Kenneth S. M.; Tsang, Alan K. L.; Shek, Chung-Tong; Wang, Ming; Choi, Garnet K. Y.; Guo, Rongtong; Wong, Beatrice H. L.; Poon, Rosana W. S.; Lam, Carol S. F.; Wang, Sylvia Y. H.; Fan, Rachel Y. Y.; Chan, Kwok-Hung; Zheng, Bo-Jian

    2012-01-01

    Although coronaviruses are known to infect various animals by adapting to new hosts, interspecies transmission events are still poorly understood. During a surveillance study from 2005 to 2010, a novel alphacoronavirus, BatCoV HKU10, was detected in two very different bat species, Ro-BatCoV HKU10 in Leschenault's rousettes (Rousettus leschenaulti) (fruit bats in the suborder Megachiroptera) in Guangdong and Hi-BatCoV HKU10 in Pomona leaf-nosed bats (Hipposideros pomona) (insectivorous bats in the suborder Microchiroptera) in Hong Kong. Although infected bats appeared to be healthy, Pomona leaf-nosed bats carrying Hi-BatCoV HKU10 had lower body weights than uninfected bats. To investigate possible interspecies transmission between the two bat species, the complete genomes of two Ro-BatCoV HKU10 and six Hi-BatCoV HKU10 strains were sequenced. Genome and phylogenetic analyses showed that Ro-BatCoV HKU10 and Hi-BatCoV HKU10 represented a novel alphacoronavirus species, sharing highly similar genomes except in the genes encoding spike proteins, which had only 60.5% amino acid identities. Evolution of the spike protein was also rapid in Hi-BatCoV HKU10 strains from 2005 to 2006 but stabilized thereafter. Molecular-clock analysis dated the most recent common ancestor of all BatCoV HKU10 strains to 1959 (highest posterior density regions at 95% [HPDs], 1886 to 2002) and that of Hi-BatCoV HKU10 to 1986 (HPDs, 1956 to 2004). The data suggested recent interspecies transmission from Leschenault's rousettes to Pomona leaf-nosed bats in southern China. Notably, the rapid adaptive genetic change in BatCoV HKU10 spike protein by ∼40% amino acid divergence after recent interspecies transmission was even greater than the ∼20% amino acid divergence between spike proteins of severe acute respiratory syndrome-related Rhinolophus bat coronavirus (SARSr-CoV) in bats and civets. This study provided the first evidence for interspecies transmission of coronavirus between bats of

  11. Actinobacterial peroxidases: an unexplored resource for biocatalysis.

    PubMed

    le Roes-Hill, Marilize; Khan, Nuraan; Burton, Stephanie Gail

    2011-07-01

    Peroxidases are redox enzymes that can be found in all forms of life where they play diverse roles. It is therefore not surprising that they can also be applied in a wide range of industrial applications. Peroxidases have been extensively studied with particular emphasis on those isolated from fungi and plants. In general, peroxidases can be grouped into haem-containing and non-haem-containing peroxidases, each containing protein families that share sequence similarity. The order Actinomycetales comprises a large group of bacteria that are often exploited for their diverse metabolic capabilities, and with recent increases in the number of sequenced genomes, it has become clear that this metabolically diverse group of organisms also represents a large resource for redox enzymes. It is therefore surprising that, to date, no review article has been written on the wide range of peroxidases found within the actinobacteria. In this review article, we focus on the different types of peroxidases found in actinobacteria, their natural role in these organisms and how they compare with the more well-described peroxidases. Finally, we also focus on work remaining to be done in this research field in order for peroxidases from actinobacteria to be applied in industrial processes.

  12. The actinobacterial colonization of Etruscan paintings.

    PubMed

    Diaz-Herraiz, Marta; Jurado, Valme; Cuezva, Soledad; Laiz, Leonila; Pallecchi, Pasquino; Tiano, Piero; Sanchez-Moral, Sergio; Saiz-Jimenez, Cesareo

    2013-01-01

    The paintings from Tomba della Scimmia, in Tuscany, are representative of the heavy bacterial colonization experienced in most Etruscan necropolises. The tomb remained open until the late 70's when it was closed because of severe deterioration of the walls, ceiling and paintings after decades of visits. The deterioration is the result of environmental changes and impacts suffered since its discovery in 1846. We show scanning electron microscopy and molecular studies that reveal the extent and nature of the biodeterioration. Actinobacteria, mainly Nocardia and Pseudonocardia colonize and grow on the tomb walls and this process is linked to the availability of organic matter, phyllosilicates (e.g. clay minerals) and iron oxides. Nocardia is found metabolically active in the paintings. The data confirm the specialization of the genera Nocardia and Pseudonocardia in the colonization of subterranean niches.

  13. The Actinobacterial Colonization of Etruscan Paintings

    PubMed Central

    Diaz-Herraiz, Marta; Jurado, Valme; Cuezva, Soledad; Laiz, Leonila; Pallecchi, Pasquino; Tiano, Piero; Sanchez-Moral, Sergio; Saiz-Jimenez, Cesareo

    2013-01-01

    The paintings from Tomba della Scimmia, in Tuscany, are representative of the heavy bacterial colonization experienced in most Etruscan necropolises. The tomb remained open until the late 70′s when it was closed because of severe deterioration of the walls, ceiling and paintings after decades of visits. The deterioration is the result of environmental changes and impacts suffered since its discovery in 1846. We show scanning electron microscopy and molecular studies that reveal the extent and nature of the biodeterioration. Actinobacteria, mainly Nocardia and Pseudonocardia colonize and grow on the tomb walls and this process is linked to the availability of organic matter, phyllosilicates (e.g. clay minerals) and iron oxides. Nocardia is found metabolically active in the paintings. The data confirm the specialization of the genera Nocardia and Pseudonocardia in the colonization of subterranean niches. PMID:23486535

  14. An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa.

    PubMed

    Zhi, Xiao-Yang; Li, Wen-Jun; Stackebrandt, Erko

    2009-03-01

    The higher ranks of the class Actinobacteria were proposed and described in 1997. At each rank, the taxa were delineated from each other solely on the basis of 16S rRNA gene sequence phylogenetic clustering and taxon-specific 16S rRNA signature nucleotides. In the past 10 years, many novel members have been assigned to this class while, at the same time, some members have been reclassified. The new 16S rRNA gene sequence information and the changes in phylogenetic positions of some taxa influence decisions about which 16S rRNA nucleotides to define as taxon-specific. As a consequence, the phylogenetic relationships of Actinobacteria at higher levels may need to be reconstructed. Here, we present new 16S rRNA signature nucleotide patterns of taxa above the family level and indicate the affiliation of genera to families. These sets replace the signatures published in 1997. In addition, Actinopolysporineae subord. nov. and Actinopolysporaceae fam. nov. are proposed to accommodate the genus Actinopolyspora, Kineosporiineae subord. nov. and Kineosporiaceae fam. nov. are proposed to accommodate the genera Kineococcus, Kineosporia and Quadrisphaera, Beutenbergiaceae fam. nov. is proposed to accommodate the genera Beutenbergia, Georgenia and Salana and Cryptosporangiaceae fam. nov. is proposed to accommodate the genus Cryptosporangium. The families Nocardiaceae and Gordoniaceae are proposed to be combined in an emended family Nocardiaceae. Emended descriptions are also proposed for most of the other higher taxa.

  15. Genus IX. Kutzneria Stackebrandt, Kroppenstedt, Jahnke, Kemmerling and Gurtler 1994, 267vp

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The physiology, systematics and ecology of the species that currently composes the actinobacterial genus Kutzneria is presented. The phylogenetic position of the species within this genus relative to the other genera within the suborder Pseudonocardineae is discussed. Methods for isolation, preser...

  16. Statistical Approaches for Estimating Actinobacterial Diversity in Marine Sediments

    PubMed Central

    Stach, James E. M.; Maldonado, Luis A.; Masson, Douglas G.; Ward, Alan C.; Goodfellow, Michael; Bull, Alan T.

    2003-01-01

    Bacterial diversity in a deep-sea sediment was investigated by constructing actinobacterium-specific 16S ribosomal DNA (rDNA) clone libraries from sediment sections taken 5 to 12, 15 to 18, and 43 to 46 cm below the sea floor at a depth of 3,814 m. Clones were placed into operational taxonomic unit (OTU) groups with ≥99% 16S rDNA sequence similarity; the cutoff value for an OTU was derived by comparing 16S rRNA homology with DNA-DNA reassociation values for members of the class Actinobacteria. Diversity statistics were used to determine how the level of dominance, species richness, and genetic diversity varied with sediment depth. The reciprocal of Simpson's index (1/D) indicated that the pattern of diversity shifted toward dominance from uniformity with increasing sediment depth. Nonparametric estimation of the species richness in the 5- to 12-, 15- to 18-, and 43- to 46-cm sediment sections revealed a trend of decreasing species number with depth, 1,406, 308, and 212 OTUs, respectively. Application of the LIBSHUFF program indicated that the 5- to 12-cm clone library was composed of OTUs significantly (P = 0.001) different from those of the 15- to 18- and 43- to 46-cm libraries. FST and phylogenetic grouping of taxa (P tests) were both significant (P < 0.00001 and P < 0.001, respectively), indicating that genetic diversity decreased with sediment depth and that each sediment community harbored unique phylogenetic lineages. It was also shown that even nonconservative OTU definitions result in severe underestimation of species richness; unique phylogenetic clades detected in one OTU group suggest that OTUs do not correspond to real ecological groups sensu Palys (T. Palys, L. K. Nakamura, and F. M. Cohan, Int. J. Syst. Bacteriol. 47:1145-1156, 1997). Mechanisms responsible for diversity and their implications are discussed. PMID:14532080

  17. Key roles for freshwater Actinobacteria revealed by deep metagenomic sequencing.

    PubMed

    Ghai, Rohit; Mizuno, Carolina Megumi; Picazo, Antonio; Camacho, Antonio; Rodriguez-Valera, Francisco

    2014-12-01

    Freshwater ecosystems are critical but fragile environments directly affecting society and its welfare. However, our understanding of genuinely freshwater microbial communities, constrained by our capacity to manipulate its prokaryotic participants in axenic cultures, remains very rudimentary. Even the most abundant components, freshwater Actinobacteria, remain largely unknown. Here, applying deep metagenomic sequencing to the microbial community of a freshwater reservoir, we were able to circumvent this traditional bottleneck and reconstruct de novo seven distinct streamlined actinobacterial genomes. These genomes represent three new groups of photoheterotrophic, planktonic Actinobacteria. We describe for the first time genomes of two novel clades, acMicro (Micrococcineae, related to Luna2,) and acAMD (Actinomycetales, related to acTH1). Besides, an aggregate of contigs belonged to a new branch of the Acidimicrobiales. All are estimated to have small genomes (approximately 1.2 Mb), and their GC content varied from 40 to 61%. One of the Micrococcineae genomes encodes a proteorhodopsin, a rhodopsin type reported for the first time in Actinobacteria. The remarkable potential capacity of some of these genomes to transform recalcitrant plant detrital material, particularly lignin-derived compounds, suggests close linkages between the terrestrial and aquatic realms. Moreover, abundances of Actinobacteria correlate inversely to those of Cyanobacteria that are responsible for prolonged and frequently irretrievable damage to freshwater ecosystems. This suggests that they might serve as sentinels of impending ecological catastrophes.

  18. Complete genome sequence of Stackebrandtia nassauensis type strain (LLR-40K-21T)

    SciTech Connect

    Munk, Chris; Lapidus, Alla; Copeland, Alex; Jando, Marlen; Mayilraj, Shanmugam; Glavina Del Rio, Tijana; Nolan, Matt; Chen, Feng; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Han, Cliff; Detter, John C.; Bruce, David; Goodwin, Lynne; Chain, Patrick; Pitluck, Sam; Göker, Markus; Ovchinikova, Galina; Pati, Amrita; Ivanova, Natalia; Mavromatis, Konstantinos; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Bristow, Jim; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter

    2009-12-30

    Stackebrandtia nassauensis Labeda and Kroppenstedt (2005) is the type species of the genus Stackebrandtia, and a member of the actinobacterial family Glycomycetaceae. Stackebrandtia currently contains two species, which are differentiated from Glycomyces spp. by cellular fatty acid and menaquinone composition. Strain LLR-40K-21T is Gram-positive, aerobic, and nonmotile, with a branched substrate mycelium and on some media an aerial mycelium. The strain was originally isolated from a soil sample collected from a road side in Nassau, Bahamas. We describe the features of this organism, together with the complete genome sequence and annotation. Lastly, this is the first complete genome sequence of the actinobacterial suborder Glycomycineae. The 6,841,557 bp long single replicon genome with its 6487 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  19. Structural characterization of ferric hemoglobins from three antarctic fish species of the suborder notothenioidei.

    PubMed

    Vergara, Alessandro; Franzese, Marisa; Merlino, Antonello; Vitagliano, Luigi; Verde, Cinzia; di Prisco, Guido; Lee, H Caroline; Peisach, Jack; Mazzarella, Lelio

    2007-10-15

    Spontaneous autoxidation of tetrameric Hbs leads to the formation of Fe (III) forms, whose physiological role is not fully understood. Here we report structural characterization by EPR of the oxidized states of tetrameric Hbs isolated from the Antarctic fish species Trematomus bernacchii, Trematomus newnesi, and Gymnodraco acuticeps, as well as the x-ray crystal structure of oxidized Trematomus bernacchii Hb, redetermined at high resolution. The oxidation of these Hbs leads to formation of states that were not usually detected in previous analyses of tetrameric Hbs. In addition to the commonly found aquo-met and hydroxy-met species, EPR analyses show that two distinct hemichromes coexist at physiological pH, referred to as hemichromes I and II, respectively. Together with the high-resolution crystal structure (1.5 A) of T. bernacchii and a survey of data available for other heme proteins, hemichrome I was assigned by x-ray crystallography and by EPR as a bis-His complex with a distorted geometry, whereas hemichrome II is a less constrained (cytochrome b5-like) bis-His complex. In four of the five Antartic fish Hbs examined, hemichrome I is the major form. EPR shows that for HbCTn, the amount of hemichrome I is substantially reduced. In addition, the concomitant presence of a penta-coordinated high-spin Fe (III) species, to our knowledge never reported before for a wild-type tetrameric Hb, was detected. A molecular modeling investigation demonstrates that the presence of the bulkier Ile in position 67beta in HbCTn in place of Val as in the other four Hbs impairs the formation of hemichrome I, thus favoring the formation of the ferric penta-coordinated species. Altogether the data show that ferric states commonly associated with monomeric and dimeric Hbs are also found in tetrameric Hbs.

  20. Big and slow: phylogenetic estimates of molecular evolution in baleen whales (suborder mysticeti).

    PubMed

    Jackson, J A; Baker, C S; Vant, M; Steel, D J; Medrano-González, L; Palumbi, S R

    2009-11-01

    Baleen whales are the largest animals that have ever lived. To develop an improved estimation of substitution rate for nuclear and mitochondrial DNA for this taxon, we implemented a relaxed-clock phylogenetic approach using three fossil calibration dates: the divergence between odontocetes and mysticetes approximately 34 million years ago (Ma), between the balaenids and balaenopterids approximately 28 Ma, and the time to most recent common ancestor within the Balaenopteridae approximately 12 Ma. We examined seven mitochondrial genomes, a large number of mitochondrial control region sequences (219 haplotypes for 465 bp) and nine nuclear introns representing five species of whales, within which multiple species-specific alleles were sequenced to account for within-species diversity (1-15 for each locus). The total data set represents >1.65 Mbp of mitogenome and nuclear genomic sequence. The estimated substitution rate for the humpback whale control region (3.9%/million years, My) was higher than previous estimates for baleen whales but slow relative to other mammal species with similar generation times (e.g., human-chimp mean rate > 20%/My). The mitogenomic third codon position rate was also slow relative to other mammals (mean estimate 1%/My compared with a mammalian average of 9.8%/My for the cytochrome b gene). The mean nuclear genomic substitution rate (0.05%/My) was substantially slower than average synonymous estimates for other mammals (0.21-0.37%/My across a range of studies). The nuclear and mitogenome rate estimates for baleen whales were thus roughly consistent with an 8- to 10-fold slowing due to a combination of large body size and long generation times. Surprisingly, despite the large data set of nuclear intron sequences, there was only weak and conflicting support for alternate hypotheses about the phylogeny of balaenopterid whales, suggesting that interspecies introgressions or a rapid radiation has obscured species relationships in the nuclear genome.

  1. Muscle metabolism and growth in Antarctic fishes (suborder Notothenioidei): evolution in a cold environment.

    PubMed

    Johnston, Ian A

    2003-12-01

    The radiation of notothenioid fishes (order Perciformes) in the Southern Ocean provides a model system for investigating evolution and adaptation to a low temperature environment. The Notothenioid fishes comprising eight families, 43 genera and 122 species dominate the fish fauna in Antarctica. The diversification of the clade probably began 15-20 million years ago after the formation of the Antarctic Polar Front. The radiation was, therefore, associated with climatic cooling down to the present day temperature of -1.86 degrees C. Origins and Evolution of the Antarctic Biota Geological Society Special Publication No. 47, Geological Society of London. pp. 253-268). The success of the group has been closely linked with the evolution of glycopeptide and peptide antifreezes, which are amongst the most abundant proteins in blood and interstitial fluid. The radiation of the clade has been associated with disaptation (evolutionary loss of function) and recovery. For example, it is thought that the icefishes (Channichyidae) lost haemoglobin through a single mutational event leading to the deletion of the entire beta-globin gene and the 5' end of the linked alpha-globin gene, resulting in compensatory adaptations of the cardiovascular system. Phylogenetically based statistical methods also indicate a progressive and dramatic reduction in the number of skeletal muscle fibres (FN(max)) at the end of the recruitment phase of growth in basal compared to derived families. The reduction in FN(max) is associated with a compensatory increase in the maximum fibre diameter, which can reach 100 microm in slow and 600 microm in fast muscle fibres. At -1 to 0 degrees C, the oxygen consumption of isolated mitochondria per mg mitochondrial protein shows no evidence of up-regulation relative to mitochondria from temperate and tropical Perciform fishes. The mitochondria content of slow muscle fibres in Antarctic notothenioids is towards the upper end of the range reported for teleosts with similar lifestyles, reaching 50% in Channichthyids. High mitochondrial densities facilitate ATP production and oxygen diffusion through the membrane lipid compartment of the fibre. Modelling studies suggest that adequate oxygen flux in the large diameter muscle fibres of notothenioids is possible because of the reduced metabolic demand and enhanced solubility of oxygen associated with low temperature. At the whole animal level size-corrected resting metabolic rate fits on the same temperature relationship as for Perciformes from warmer climates. It seems likely that the additional energetic costs associated with antifreeze synthesis and high mitochondrial densities are compensated for by reductions in other energy requiring processes: a hypothesis that could be tested with detailed energy budget studies. One plausible candidate is a reduction in membrane leak pathways linked to the loss of muscle fibres, which would serve to minimise the cost of maintaining ionic gradients.

  2. Korean indigenous bacterial species with valid names belonging to the phylum Actinobacteria.

    PubMed

    Bae, Kyung Sook; Kim, Mi Sun; Lee, Ji Hee; Kang, Joo Won; Kim, Dae In; Lee, Ji Hee; Seong, Chi Nam

    2016-12-01

    To understand the isolation and classification state of actinobacterial species with valid names for Korean indigenous isolates, isolation source, regional origin, and taxonomic affiliation of the isolates were studied. At the time of this writing, the phylum Actinobacteria consisted of only one class, Actinobacteria, including five subclasses, 10 orders, 56 families, and 330 genera. Moreover, new taxa of this phylum continue to be discovered. Korean actinobacterial species with a valid name has been reported from 1995 as Tsukamurella inchonensis isolated from a clinical specimen. In 1997, Streptomyces seoulensis was validated with the isolate from the natural Korean environment. Until Feb. 2016, 256 actinobacterial species with valid names originated from Korean territory were listed on LPSN. The species were affiliated with three subclasses (Acidimicrobidae, Actinobacteridae, and Rubrobacteridae), four orders (Acidimicrobiales, Actinomycetales, Bifidobacteriales, and Solirubrobacterales), 12 suborders, 36 families, and 93 genera. Most of the species belonged to the subclass Actinobacteridae, and almost of the members of this subclass were affiliated with the order Actinomycetales. A number of novel isolates belonged to the families Nocardioidaceae, Microbacteriaceae, Intrasporangiaceae, and Streptomycetaceae as well as the genera Nocardioides, Streptomyces, and Microbacterium. Twenty-six novel genera and one novel family, Motilibacteraceae, were created first with Korean indigenous isolates. Most of the Korean indigenous actionobacterial species were isolated from natural environments such as soil, seawater, tidal flat sediment, and fresh-water. A considerable number of species were isolated from artificial resources such as fermented foods, wastewater, compost, biofilm, and water-cooling systems or clinical specimens. Korean indigenous actinobacterial species were isolated from whole territory of Korea, and especially a large number of species were from Jeju

  3. Actinobacterial Acyl Coenzyme A Synthetases Involved in Steroid Side-Chain Catabolism

    PubMed Central

    Casabon, Israël; Swain, Kendra; Crowe, Adam M.

    2014-01-01

    Bacterial steroid catabolism is an important component of the global carbon cycle and has applications in drug synthesis. Pathways for this catabolism involve multiple acyl coenzyme A (CoA) synthetases, which activate alkanoate substituents for β-oxidation. The functions of these synthetases are poorly understood. We enzymatically characterized four distinct acyl-CoA synthetases from the cholate catabolic pathway of Rhodococcus jostii RHA1 and the cholesterol catabolic pathway of Mycobacterium tuberculosis. Phylogenetic analysis of 70 acyl-CoA synthetases predicted to be involved in steroid metabolism revealed that the characterized synthetases each represent an orthologous class with a distinct function in steroid side-chain degradation. The synthetases were specific for the length of alkanoate substituent. FadD19 from M. tuberculosis H37Rv (FadD19Mtb) transformed 3-oxo-4-cholesten-26-oate (kcat/Km = 0.33 × 105 ± 0.03 × 105 M−1 s−1) and represents orthologs that activate the C8 side chain of cholesterol. Both CasGRHA1 and FadD17Mtb are steroid-24-oyl-CoA synthetases. CasG and its orthologs activate the C5 side chain of cholate, while FadD17 and its orthologs appear to activate the C5 side chain of one or more cholesterol metabolites. CasIRHA1 is a steroid-22-oyl-CoA synthetase, representing orthologs that activate metabolites with a C3 side chain, which accumulate during cholate catabolism. CasI had similar apparent specificities for substrates with intact or extensively degraded steroid nuclei, exemplified by 3-oxo-23,24-bisnorchol-4-en-22-oate and 1β(2′-propanoate)-3aα-H-4α(3″-propanoate)-7aβ-methylhexahydro-5-indanone (kcat/Km = 2.4 × 105 ± 0.1 × 105 M−1 s−1 and 3.2 × 105 ± 0.3 × 105 M−1 s−1, respectively). Acyl-CoA synthetase classes involved in cholate catabolism were found in both Actinobacteria and Proteobacteria. Overall, this study provides insight into the physiological roles of acyl-CoA synthetases in steroid catabolism and a phylogenetic classification enabling prediction of specific functions of related enzymes. PMID:24244004

  4. The actinobacterial transcription factor RbpA binds to the principal sigma subunit of RNA polymerase.

    PubMed

    Tabib-Salazar, Aline; Liu, Bing; Doughty, Philip; Lewis, Richard A; Ghosh, Somadri; Parsy, Marie-Laure; Simpson, Peter J; O'Dwyer, Kathleen; Matthews, Steve J; Paget, Mark S

    2013-06-01

    RbpA is a small non-DNA-binding transcription factor that associates with RNA polymerase holoenzyme and stimulates transcription in actinobacteria, including Streptomyces coelicolor and Mycobacterium tuberculosis. RbpA seems to show specificity for the vegetative form of RNA polymerase as opposed to alternative forms of the enzyme. Here, we explain the basis of this specificity by showing that RbpA binds directly to the principal σ subunit in these organisms, but not to more diverged alternative σ factors. Nuclear magnetic resonance spectroscopy revealed that, although differing in their requirement for structural zinc, the RbpA orthologues from S. coelicolor and M. tuberculosis share a common structural core domain, with extensive, apparently disordered, N- and C-terminal regions. The RbpA-σ interaction is mediated by the C-terminal region of RbpA and σ domain 2, and S. coelicolor RbpA mutants that are defective in binding σ are unable to stimulate transcription in vitro and are inactive in vivo. Given that RbpA is essential in M. tuberculosis and critical for growth in S. coelicolor, these data support a model in which RbpA plays a key role in the σ cycle in actinobacteria.

  5. Complete genome sequence of Actinosynnema mirum type strain (101T)

    SciTech Connect

    Land, Miriam; Lapidus, Alla; Mayilraj, Shanmugam; Chen, Feng; Copeland, Alex; Glavina Del Rio, Tijana; Nolan, Matt; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Chertkov, Olga; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Rohde, Manfred; Goker, Markus; Pati, Amrita; Ivanova, Natalia; Mavrommatis, Konstantinos; Chen, Amy; Palaniappan, Krishna; Hauser, Loren; Chang, Yun-Juan; Jefferies, Cynthia; Brettin, Thomas; Detter, John C.; Han, Cliff; Chain, Patrick; Tindall, Brian; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter

    2009-05-20

    Actinosynnema mirum Hasegawa et al. 1978 is the type species of the genus, and is of phylogenetic interest because of its central phylogenetic location in the Actino-synnemataceae, a rapidly growing family within the actinobacterial suborder Pseudo-nocardineae. A. mirum is characterized by its motile spores borne on synnemata and as a producer of nocardicin antibiotics. It is capable of growing aerobically and under a moderate CO2 atmosphere. The strain is a Gram-positive, aerial and substrate mycelium producing bacterium, originally isolated from a grass blade collected from the Raritan River, New Jersey. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the family Actinosynnemataceae, and only the second sequence from the actinobacterial suborder Pseudonocardineae. The 8,248,144 bp long single replicon genome with its 7100 protein-coding and 77 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  6. Complete genome sequence of Actinosynnema mirum type strain (101T)

    SciTech Connect

    Land, Miriam L; Lapidus, Alla L.; Mayilraj, Shanmugam; Chen, Feng; Copeland, A; Glavina Del Rio, Tijana; Nolan, Matt; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Chertkov, Olga; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Rohde, Manfred; Goker, Markus; Pati, Amrita; Ivanova, N; Mavromatis, K; Chen, Amy; Palaniappan, Krishna; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Brettin, Thomas S; Detter, J. Chris; Han, Cliff; Chain, Patrick S. G.; Tindall, Brian; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2009-01-01

    Actinosynnema mirum Hasegawa et al. 1978 is the type species of the genus, and is of phylogenetic interest because of its central phylogenetic location in the Actino-synnemataceae, a rapidly growing family within the actinobacterial suborder Pseudo-nocardineae. A. mirum is characterized by its motile spores borne on synnemata and as a producer of nocardicin antibiotics. It is capable of growing aerobically and under a moderate CO2 atmosphere. The strain is a Gram-positive, aerial and substrate mycelium producing bacterium, originally isolated from a grass blade collected from the Raritan River, New Jersey. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the family Actinosynnemataceae, and only the second sequence from the actinobacterial suborder Pseudonocardineae. The 8,248,144 bp long single replicon genome with its 7100 protein-coding and 77 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  7. Thalassiella azotovora gen. nov., sp. nov., a New Member of the Family Kineosporiaceae Isolated from Sea Water in South Korea.

    PubMed

    Lee, Dongwook; Jang, Jun Hyeong; Cha, Seho; Seo, Taegun

    2016-11-01

    A gram-positive, nonmotile, rod-shaped, nonflagellated, aerobic bacterium, designated strain DSD2(T) was isolated from a seawater sample from Sadong wharf, Ulleung-Island, South Korea. Strain DSD2(T) was found to be able to grow at pH ranging from 6 to 11 (optimum 7-8), 0-7 % (w/v) NaCl (optimum 0 %), at 10-42 °C (optimum 37 °C). 16S rRNA gene sequence analysis revealed that strain DSD2(T) was 95.8 % similar to the type strain of Kineosporia rhamnosa KACC 15195(T), 95.8 % similar to Angustibacter aerolatus KACC 15527(T), and 95.5 % similar to Kineococcus xinjiangensis KCTC 19474(T) as its closest relatives. A neighbor-joining phylogenetic tree based on the 16S rRNA gene sequence showed that strain DSD2(T) related to Micrococcineae and Kineosporiineae suborder clade. The major polar lipids were phosphoglycolipids and phospholipids. Strain DSD2(T) was found to contain MK-8 (H2) and MK-9 (H4) as the predominant menaquinone and iso-C16:0 as the major fatty acid. The isolate contained meso-diaminopimelic acid (meso-A2pm) with alanine, glutamic acid, and glycine as the diagnostic diamino acid. The DNA G+C content of strain DSD2(T) was 73.2 mol%. On the basis of phylogenetic, biochemical, chemotaxonomic, and other physiological characteristics, strain DSD2(T) is assigned to a novel species of a novel genus within the suborder Kineosporiineae and the name Thalassiella azotovora gen nov., sp. nov., is proposed. The type strain is DSD2(T) (= KCTC 39634(T) = JCM 31134(T)).

  8. Soil Bacterial Community Shifts after Chitin Enrichment: An Integrative Metagenomic Approach

    PubMed Central

    Jacquiod, Samuel; Franqueville, Laure; Cécillon, Sébastien; M. Vogel, Timothy; Simonet, Pascal

    2013-01-01

    Chitin is the second most produced biopolymer on Earth after cellulose. Chitin degrading enzymes are promising but untapped sources for developing novel industrial biocatalysts. Hidden amongst uncultivated micro-organisms, new bacterial enzymes can be discovered and exploited by metagenomic approaches through extensive cloning and screening. Enrichment is also a well-known strategy, as it allows selection of organisms adapted to feed on a specific compound. In this study, we investigated how the soil bacterial community responded to chitin enrichment in a microcosm experiment. An integrative metagenomic approach coupling phylochips and high throughput shotgun pyrosequencing was established in order to assess the taxonomical and functional changes in the soil bacterial community. Results indicate that chitin enrichment leads to an increase of Actinobacteria, γ-proteobacteria and β-proteobacteria suggesting specific selection of chitin degrading bacteria belonging to these classes. Part of enriched bacterial genera were not yet reported to be involved in chitin degradation, like the members from the Micrococcineae sub-order (Actinobacteria). An increase of the observed bacterial diversity was noticed, with detection of specific genera only in chitin treated conditions. The relative proportion of metagenomic sequences related to chitin degradation was significantly increased, even if it represents only a tiny fraction of the sequence diversity found in a soil metagenome. PMID:24278158

  9. Evolution of dosage compensation in Diptera: the gene maleless implements dosage compensation in Drosophila (Brachycera suborder) but its homolog in Sciara (Nematocera suborder) appears to play no role in dosage compensation.

    PubMed

    Ruiz, M F; Esteban, M R; Doñoro, C; Goday, C; Sánchez, L

    2000-12-01

    In Drosophila melanogaster and in Sciara ocellaris dosage compensation occurs by hypertranscription of the single male X chromosome. This article reports the cloning and characterization in S. ocellaris of the gene homologous to maleless (mle) of D. melanogaster, which implements dosage compensation. The Sciara mle gene produces a single transcript, encoding a helicase, which is present in both male and female larvae and adults and in testes and ovaries. Both Sciara and Drosophila MLE proteins are highly conserved. The affinity-purified antibody to D. melanogaster MLE recognizes the S. ocellaris MLE protein. In contrast to Drosophila polytene chromosomes, where MLE is preferentially associated with the male X chromosome, in Sciara MLE is found associated with all chromosomes. Anti-MLE staining of Drosophila postblastoderm male embryos revealed a single nuclear dot, whereas Sciara male and female embryos present multiple intranuclear staining spots. This expression pattern in Sciara is also observed before blastoderm stage, when dosage compensation is not yet set up. The affinity-purified antibodies against D. melanogaster MSL1, MSL3, and MOF proteins involved in dosage compensation also revealed no differences in the staining pattern between the X chromosome and the autosomes in both Sciara males and females. These results lead us to propose that different proteins in Drosophila and Sciara would implement dosage compensation.

  10. Evolution of dosage compensation in Diptera: the gene maleless implements dosage compensation in Drosophila (Brachycera suborder) but its homolog in Sciara (Nematocera suborder) appears to play no role in dosage compensation.

    PubMed Central

    Ruiz, M F; Esteban, M R; Doñoro, C; Goday, C; Sánchez, L

    2000-01-01

    In Drosophila melanogaster and in Sciara ocellaris dosage compensation occurs by hypertranscription of the single male X chromosome. This article reports the cloning and characterization in S. ocellaris of the gene homologous to maleless (mle) of D. melanogaster, which implements dosage compensation. The Sciara mle gene produces a single transcript, encoding a helicase, which is present in both male and female larvae and adults and in testes and ovaries. Both Sciara and Drosophila MLE proteins are highly conserved. The affinity-purified antibody to D. melanogaster MLE recognizes the S. ocellaris MLE protein. In contrast to Drosophila polytene chromosomes, where MLE is preferentially associated with the male X chromosome, in Sciara MLE is found associated with all chromosomes. Anti-MLE staining of Drosophila postblastoderm male embryos revealed a single nuclear dot, whereas Sciara male and female embryos present multiple intranuclear staining spots. This expression pattern in Sciara is also observed before blastoderm stage, when dosage compensation is not yet set up. The affinity-purified antibodies against D. melanogaster MSL1, MSL3, and MOF proteins involved in dosage compensation also revealed no differences in the staining pattern between the X chromosome and the autosomes in both Sciara males and females. These results lead us to propose that different proteins in Drosophila and Sciara would implement dosage compensation. PMID:11102379

  11. Complete mitochondrial genome of brown marmorated stink bug Halyomorpha halys (Hemiptera: Pentatomidae) and phylogenetic relationships of Hemipteran suborders

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The newly sequenced complete mitochondrial genome of the brown marmorated stink bug, Halyomorpha halys (Stal) (Hemiptera: Pentatomidae), is a circular molecule of 16,518 bp with a total A+T content of 76.4% and two extensive repeat regions in A+T rich region. Nucleotide composition and codon usage ...

  12. Molecular analysis and developmental expression of the Sex-lethal gene of Sciara ocellaris (Diptera order, Nematocera suborder).

    PubMed

    Ruiz, M F; Goday, C; González, P; Sánchez, L

    2003-06-01

    This paper reports the cloning and characterization in Sciara ocellaris of the gene homologous to Sex-lethal (Sxl) of Drosophila melanogaster. This gene plays the key role controlling sex determination and dosage compensation in the latter species. The Sciara Sxl gene produces a single transcript encoding a single protein in both males and females. This protein, found inside the nucleus, is expressed in all tissues. Both Sciara and Drosophila Sxl proteins are highly conserved at their two RNA-binding domains. In both Sciara sexes, the Sxl protein co-localizes with transcription-active regions dependent on RNA polymerase II but not on RNA polymerase I. It would appear that in Sciara, Sxl does not appear to play the key discriminative role in controlling sex determination and dosage compensation that it plays in Drosophila.

  13. The gene Sex-lethal of the Sciaridae family (order Diptera, suborder Nematocera) and its phylogeny in dipteran insects.

    PubMed

    Serna, Esther; Gorab, Eduardo; Ruiz, M Fernanda; Goday, Clara; Eirín-López, José M; Sánchez, Lucas

    2004-10-01

    This article reports the cloning and characterization of the gene homologous to Sex-lethal (Sxl) of Drosophila melanogaster from Sciara coprophila, Rhynchosciara americana, and Trichosia pubescens. This gene plays the key role in controlling sex determination and dosage compensation in D. melanogaster. The Sxl gene of the three species studied produces a single transcript encoding a single protein in both males and females. Comparison of the Sxl proteins of these Nematocera insects with those of the Brachycera showed their two RNA-binding domains (RBD) to be highly conserved, whereas significant variation was observed in both the N- and C-terminal domains. The great majority of nucleotide changes in the RBDs were synonymous, indicating that purifying selection is acting on them. In both sexes of the three Nematocera insects, the Sxl protein colocalized with transcription-active regions dependent on RNA polymerase II but not on RNA polymerase I. Together, these results indicate that Sxl does not appear to play a discriminatory role in the control of sex determination and dosage compensation in nematocerans. Thus, in the phylogenetic lineage that gave rise to the drosophilids, evolution coopted for the Sxl gene, modified it, and converted it into the key gene controlling sex determination and dosage compensation. At the same time, however, certain properties of the recruited ancestral Sxl gene were beneficial, and these are maintained in the evolved Sxl gene, allowing it to exert its sex-determining and dose compensation functions in Drosophila.

  14. Post-embryonic development in the mite suborder Opilioacarida, with notes on segmental homology in Parasitiformes (Arachnida).

    PubMed

    Klompen, Hans; Vázquez, Ma Magdalena; Bernardi, Leopoldo Ferreira de Oliveira

    2015-10-01

    In order to study homology among the major lineages of the mite (super)order Parasitiformes, developmental patterns in Opilioacarida are documented, emphasizing morphology of the earliest, post-embryonic instars. Developmental patterns are summarized for all external body structures, based on examination of material in four different genera. Development includes an egg, a 6-legged prelarva and larva, three 8-legged nymphal instars, and the adults, for the most complete ontogenetic sequence in Parasitiformes. The prelarva and larva appear to be non-feeding. Examination of cuticular structures over ontogeny allows development of an updated model for body segmentation and sensillar distribution patterns in Opilioacarida. This model includes a body made up of a well-developed ocular segment plus at most 17 additional segments. In the larvae and protonymphs each segment may carry up to six pairs of sensilla (setae or lyrifissures) arranged is distinct series (J, Z, S, Sv, Zv, Jv). The post-protonymphal instars add two more series (R and Rv) but no extra segments. This basic model is compatible with sensillar patterns in other Parasitiformes, leading to the hypothesis that all taxa in that (super)order may have the same segmental ground plan. The substantial segmental distortion implied in the model can be explained using a single process involving differential growth in the coxal regions of all appendage-bearing segments.

  15. Taxonomy of intertidal cheilostome Bryozoa of Maceió, northeastern Brazil. Part 1: Suborders Inovicellina, Malacostegina and Thalamoporellina.

    PubMed

    Vieira, Leandro M; Almeida, Ana C S; Winston, Judith E

    2016-03-29

    Thirteen cheilostome bryozoan species from intertidal habitats of Maceió, Alagoas State, Brazil, are reported here. We describe four new species: Aetea cultrata n. sp., Biflustra marcusi n. sp., Biflustra sphinx n. sp. and Jellyella brasiliensis n. sp. Two other species of Inovicellina, Aetea arcuata Winston & Hayward, 2012, and Aetea curta Jullien, 1888, and four species of Malacostegina, Arbocuspis bellula (Hincks, 1881), Arbocuspis bicornis (Hincks, 1881), Arbocuspis ramosa (Osburn, 1940), and Jellyella tuberculata (Bosc, 1802), are reported on drift algae. Three species of Thalamoporellina are found for the first time in Maceió, Labioporella tuberculata Winston, Vieira & Woollacoot, 2014, Steginoporella           magnilabris (Busk, 1854) and Thalamoporella floridana Osburn, 1940.

  16. Diversity and duplication of DQB and DRB-like genes of the MHC in baleen whales (suborder: Mysticeti).

    PubMed

    Baker, C S; Vant, M D; Dalebout, M L; Lento, G M; O'Brien, S J; Yuhki, N

    2006-05-01

    The molecular diversity and phylogenetic relationships of two class II genes of the baleen whale major histocompatibility complex were investigated and compared to toothed whales and out-groups. Amplification of the DQB exon 2 provided sequences showing high within-species and between-species nucleotide diversity and uninterrupted reading frames consistent with functional class II loci found in related mammals (e.g., ruminants). Cloning of amplified products indicated gene duplication in the humpback whale and triplication in the southern right whale, with average nucleotide diversity of 5.9 and 6.3%, respectively, for alleles of each species. Significantly higher nonsynonymous divergence at sites coding for peptide binding (32% for humpback and 40% for southern right) suggested that these loci were subject to positive (overdominant) selection. A population survey of humpback whales detected 23 alleles, differing by up to 21% of their inferred amino acid sequences. Amplification of the DRB exon 2 resulted in two groups of sequences. One was most similar to the DRB3 of the cow and present in all whales screened to date, including toothed whales. The second was most similar to the DRB2 of the cow and was found only in the bowhead and right whales. Both loci showed low diversity among species and apparent loss of function or altered function including interruption of reading frames. Finally, comparison of inferred protein sequence of the DRB3-like locus suggested convergence with the DQB, perhaps resulting from intergenic conversion or recombination.

  17. Comparative Community Proteomics Demonstrates the Unexpected Importance of Actinobacterial Glycoside Hydrolase Family 12 Protein for Crystalline Cellulose Hydrolysis

    SciTech Connect

    Hiras, Jennifer; Wu, Yu-Wei; Deng, Kai; Nicora, Carrie D.; Aldrich, Joshua T.; Frey, Dario; Kolinko, Sebastian; Robinson, Errol W.; Jacobs, Jon M.; Adams, Paul D.; Northen, Trent R.; Simmons, Blake A.; Singer, Steven W.

    2016-08-23

    ABSTRACT

    Glycoside hydrolases (GHs) are key enzymes in the depolymerization of plant-derived cellulose, a process central to the global carbon cycle and the conversion of plant biomass to fuels and chemicals. A limited number of GH families hydrolyze crystalline cellulose, often by a processive mechanism along the cellulose chain. During cultivation of thermophilic cellulolytic microbial communities, substantial differences were observed in the crystalline cellulose saccharification activities of supernatants recovered from divergent lineages. Comparative community proteomics identified a set of cellulases from a population closely related to actinobacteriumThermobispora bisporathat were highly abundant in the most active consortium. Among the cellulases fromT. bispora, the abundance of a GH family 12 (GH12) protein correlated most closely with the changes in crystalline cellulose hydrolysis activity. This result was surprising since GH12 proteins have been predominantly characterized as enzymes active on soluble polysaccharide substrates. Heterologous expression and biochemical characterization of the suite ofT. bisporahydrolytic cellulases confirmed that the GH12 protein possessed the highest activity on multiple crystalline cellulose substrates and demonstrated that it hydrolyzes cellulose chains by a predominantly random mechanism. This work suggests that the role of GH12 proteins in crystalline cellulose hydrolysis by cellulolytic microbes should be reconsidered.

    IMPORTANCECellulose is the most abundant organic polymer on earth, and its enzymatic hydrolysis is a key reaction in the global carbon cycle and the conversion of plant biomass to biofuels. The glycoside hydrolases that depolymerize crystalline cellulose have been primarily characterized from isolates. In this study, we demonstrate that adapting microbial consortia from compost to grow on crystalline cellulose generated communities whose soluble enzymes exhibit differential abilities to hydrolyze crystalline cellulose. Comparative proteomics of these communities identified a protein of glycoside hydrolase family 12 (GH12), a family of proteins previously observed to primarily hydrolyze soluble substrates, as a candidate that accounted for some of the differences in hydrolytic activities. Heterologous expression confirmed that the GH12 protein identified by proteomics was active on crystalline cellulose and hydrolyzed cellulose by a random mechanism, in contrast to most cellulases that act on the crystalline polymer in a processive mechanism.

  18. Chitin amendment increases soil suppressiveness toward plant pathogens and modulates the actinobacterial and oxalobacteraceal communities in an experimental agricultural field.

    PubMed

    Cretoiu, Mariana Silvia; Korthals, Gerard W; Visser, Johnny H M; van Elsas, Jan Dirk

    2013-09-01

    A long-term experiment on the effect of chitin addition to soil on the suppression of soilborne pathogens was set up and monitored for 8 years in an experimental field, Vredepeel, The Netherlands. Chitinous matter obtained from shrimps was added to soil top layers on two different occasions, and the suppressiveness of soil toward Verticillium dahliae, as well as plant-pathogenic nematodes, was assessed, in addition to analyses of the abundances and community structures of members of the soil microbiota. The data revealed that chitin amendment had raised the suppressiveness of soil, in particular toward Verticillium dahliae, 9 months after the (second) treatment, extending to 2 years following treatment. Moreover, major effects of the added chitin on the soil microbial communities were detected. First, shifts in both the abundances and structures of the chitin-treated soil microbial communities, both of total soil bacteria and fungi, were found. In addition, the abundances and structures of soil actinobacteria and the Oxalobacteraceae were affected by chitin. At the functional gene level, the abundance of specific (family-18 glycoside hydrolase) chitinase genes carried by the soil bacteria also revealed upshifts as a result of the added chitin. The effects of chitin noted for the Oxalobacteraceae were specifically related to significant upshifts in the abundances of the species Duganella violaceinigra and Massilia plicata. These effects of chitin persisted over the time of the experiment.

  19. Comparative Community Proteomics Demonstrates the Unexpected Importance of Actinobacterial Glycoside Hydrolase Family 12 Protein for Crystalline Cellulose Hydrolysis

    PubMed Central

    Hiras, Jennifer; Wu, Yu-Wei; Deng, Kai; Nicora, Carrie D.; Aldrich, Joshua T.; Frey, Dario; Kolinko, Sebastian; Robinson, Errol W.; Jacobs, Jon M.; Adams, Paul D.; Northen, Trent R.; Simmons, Blake A.

    2016-01-01

    ABSTRACT Glycoside hydrolases (GHs) are key enzymes in the depolymerization of plant-derived cellulose, a process central to the global carbon cycle and the conversion of plant biomass to fuels and chemicals. A limited number of GH families hydrolyze crystalline cellulose, often by a processive mechanism along the cellulose chain. During cultivation of thermophilic cellulolytic microbial communities, substantial differences were observed in the crystalline cellulose saccharification activities of supernatants recovered from divergent lineages. Comparative community proteomics identified a set of cellulases from a population closely related to actinobacterium Thermobispora bispora that were highly abundant in the most active consortium. Among the cellulases from T. bispora, the abundance of a GH family 12 (GH12) protein correlated most closely with the changes in crystalline cellulose hydrolysis activity. This result was surprising since GH12 proteins have been predominantly characterized as enzymes active on soluble polysaccharide substrates. Heterologous expression and biochemical characterization of the suite of T. bispora hydrolytic cellulases confirmed that the GH12 protein possessed the highest activity on multiple crystalline cellulose substrates and demonstrated that it hydrolyzes cellulose chains by a predominantly random mechanism. This work suggests that the role of GH12 proteins in crystalline cellulose hydrolysis by cellulolytic microbes should be reconsidered. PMID:27555310

  20. Chitin Amendment Increases Soil Suppressiveness toward Plant Pathogens and Modulates the Actinobacterial and Oxalobacteraceal Communities in an Experimental Agricultural Field

    PubMed Central

    Cretoiu, Mariana Silvia; Korthals, Gerard W.; Visser, Johnny H. M.

    2013-01-01

    A long-term experiment on the effect of chitin addition to soil on the suppression of soilborne pathogens was set up and monitored for 8 years in an experimental field, Vredepeel, The Netherlands. Chitinous matter obtained from shrimps was added to soil top layers on two different occasions, and the suppressiveness of soil toward Verticillium dahliae, as well as plant-pathogenic nematodes, was assessed, in addition to analyses of the abundances and community structures of members of the soil microbiota. The data revealed that chitin amendment had raised the suppressiveness of soil, in particular toward Verticillium dahliae, 9 months after the (second) treatment, extending to 2 years following treatment. Moreover, major effects of the added chitin on the soil microbial communities were detected. First, shifts in both the abundances and structures of the chitin-treated soil microbial communities, both of total soil bacteria and fungi, were found. In addition, the abundances and structures of soil actinobacteria and the Oxalobacteraceae were affected by chitin. At the functional gene level, the abundance of specific (family-18 glycoside hydrolase) chitinase genes carried by the soil bacteria also revealed upshifts as a result of the added chitin. The effects of chitin noted for the Oxalobacteraceae were specifically related to significant upshifts in the abundances of the species Duganella violaceinigra and Massilia plicata. These effects of chitin persisted over the time of the experiment. PMID:23811512

  1. Development of an Unnatural Amino Acid Incorporation System in the Actinobacterial Natural Product Producer Streptomyces venezuelae ATCC 15439.

    PubMed

    He, Jingxuan; Van Treeck, Briana; Nguyen, Han B; Melançon, Charles E

    2016-02-19

    Many Actinobacteria, most notably Streptomyces, produce structurally diverse bioactive natural products, including ribosomally synthesized peptides, by multistep enzymatic pathways. The use of site-specific genetic incorporation of unnatural amino acids to investigate and manipulate the functions of natural product biosynthetic enzymes, enzyme complexes, and ribosomally derived peptides in these organisms would have important implications for drug discovery and development efforts. Here, we have designed, constructed, and optimized unnatural amino acid systems capable of incorporating p-iodo-l-phenylalanine and p-azido-l-phenylalanine site-specifically into proteins in the model natural product producer Streptomyces venezuelae ATCC 15439. We observed notable differences in the fidelity and efficiency of these systems between S. venezuelae and previously used hosts. Our findings serve as a foundation for using an expanded genetic code in Streptomyces to address questions related to natural product biosynthesis and mechanism of action that are relevant to drug discovery and development.

  2. Development of an Unnatural Amino Acid Incorporation System in the Actinobacterial Natural Product Producer Streptomyces venezuelae ATCC 15439

    PubMed Central

    He, Jingxuan; Van Treeck, Briana; Nguyen, Han B.; Melançon, Charles E.

    2016-01-01

    Many Actinobacteria, most notably Streptomyces, produce structurally diverse bioactive natural products, including ribosomally synthesized peptides, by multistep enzymatic pathways. The use of site-specific genetic incorporation of unnatural amino acids to investigate and manipulate the functions of natural product biosynthetic enzymes, enzyme complexes, and ribosomally-derived peptides in these organisms would have important implications for drug discovery and development efforts. Here, we have designed, constructed, and optimized unnatural amino acid systems capable of incorporating p-iodo-l-phenylalanine and p-azido-l-phenylalanine site-specifically into proteins in the model natural product producer Streptomyces venezuelae ATCC 15439. We observed notable differences in the fidelity and efficiency of these systems between S. venezuelae and previously used hosts. Our findings serve as a foundation for using an expanded genetic code in Streptomyces to address questions related to natural product biosynthesis and mechanism of action that are relevant to drug discovery and development. PMID:26562751

  3. Complete genome sequence of Catenulispora acidiphila type strain (ID 139908T)

    SciTech Connect

    Copeland, Alex; Lapidus, Alla; Rio, Tijana GlavinaDel; Nolan, Matt; Lucas, Susan; Chen, Feng; Tice, Hope; Cheng, Jan-Fang; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Mikhailova, Natalia; Pati, Amrita; Ivanova, Natalia; Mavromatis, Konstantinos; Chen, Amy; Palaniappan, Krishna; Chain, Patrick; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jefferies, Cynthia C.; Chertkov, Olga; Brettin, Thomas; Detter, John C.; Han, Cliff; Ali, Zahid; Tindall, Brian J.; Goker, Markus; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter

    2009-05-20

    Catenulispora acidiphila Busti et al. 2006 is the type species of the genus Catenulispora, and is of interest because of the rather isolated phylogenetic location of the genomically little studied suborder Catenulisporineae within the order Actinomycetales. C. acidiphilia is known for its acidophilic, aerobic lifestyle, but can also grow scantly under anaerobic conditions. Under regular conditions C. acidiphilia grows in long filaments of relatively short aerial hyphae with marked septation. It is a free living, non motile, Gram-positive bacterium isolated from a forest soil sample taken from a wooded area in Gerenzano, Italy. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of the actinobacterial family Catenulisporaceae, and the 10,467,782 bp long single replicon genome with its 9056 protein-coding and 69 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  4. Complete genome sequence of Nakamurella multipartita type strain (Y-104).

    PubMed

    Tice, Hope; Mayilraj, Shanmugam; Sims, David; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Glavina Del Rio, Tijana; Copeland, Alex; Cheng, Jan-Fang; Meincke, Linda; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavromatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D; Detter, John C; Brettin, Thomas; Rohde, Manfred; Göker, Markus; Bristow, Jim; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Chen, Feng

    2010-03-30

    Nakamurella multipartita (Yoshimi et al. 1996) Tao et al. 2004 is the type species of the monospecific genus Nakamurella in the actinobacterial suborder Frankineae. The nonmotile, coccus-shaped strain was isolated from activated sludge acclimated with sugar-containing synthetic wastewater, and is capable of accumulating large amounts of polysaccharides in its cells. Here we describe the features of the organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the family Nakamurellaceae. The 6,060,298 bp long single replicon genome with its 5415 protein-coding and 56 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  5. Histologic, Molecular, and Clinical Evaluation of Explanted Breast Prostheses, Capsules, and Acellular Dermal Matrices for Bacteria

    PubMed Central

    Poppler, Louis; Cohen, Justin; Dolen, Utku Can; Schriefer, Andrew E.; Tenenbaum, Marissa M.; Deeken, Corey; Chole, Richard A.; Myckatyn, Terence M.

    2015-01-01

    Background Subclinical infections, manifest as biofilms, are considered an important cause of capsular contracture. Acellular dermal matrices (ADMs) are frequently used in revision surgery to prevent recurrent capsular contractures. Objective We sought to identify an association between capsular contracture and biofilm formation on breast prostheses, capsules, and ADMs in a tissue expander/implant (TE/I) exchange clinical paradigm. Methods Biopsies of the prosthesis, capsule, and ADM from patients (N = 26) undergoing TE/I exchange for permanent breast implant were evaluated for subclinical infection. Capsular contracture was quantified with Baker Grade and intramammary pressure. Biofilm formation was evaluated with specialized cultures, rtPCR, bacterial taxonomy, live:dead staining, and scanning electron microscopy (SEM). Collagen distribution, capsular histology, and ADM remodeling were quantified following fluorescent and light microscopy. Results Prosthetic devices were implanted from 91 to 1115 days. Intramammary pressure increased with Baker Grade. Of 26 patients evaluated, one patient had a positive culture and one patient demonstrated convincing evidence of biofilm morphology on SEM. Following PCR amplification 5 samples randomly selected for 16S rRNA gene sequencing demonstrated an abundance of suborder Micrococcineae, consistent with contamination. Conclusions Our data suggest that bacterial biofilms likely contribute to a proportion, but not all diagnosed capsular contractures. Biofilm formation does not appear to differ significantly between ADMs or capsules. While capsular contracture remains an incompletely understood but common problem in breast implant surgery, advances in imaging, diagnostic, and molecular techniques can now provide more sophisticated insights into the pathophysiology of capsular contracture. Level of Evidence PMID:26229126

  6. Evolution of a Neotropical marine fish lineage (Subfamily Chaenopsinae, Suborder Blennioidei) based on phylogenetic analysis of combined molecular and morphological data.

    PubMed

    Lin, Hsiu-Chin; Hastings, Philip A

    2011-08-01

    Phylogenetic relationships within tube blennies (Chaenopsinae) were reconstructed using Bayesian, maximum parsimony and likelihood analyses of multiple molecular markers (mitochondrial DNA: COI; nuclear DNA: TMO-4C4, RAG1, Rhodopsin, and Histone H3) and 148 morphological characters. This total-evidence based topology is well-resolved and congruent across analytical methods with strong support for the monophyly of the Chaenopsinae, all included genera and several internal nodes. A rapid radiation in the early evolution of chaenopsins is inferred from the relatively poor support values for relationships among basal lineages and their divergence into different habitats (rocky reefs, coral reefs and the reef/sand interface). Rates of molecular evolution in chaenopsins, as inferred by divergence among four putative transisthmian geminate species pairs, are rapid compared to other fishes. Conflicts among genetic markers and morphology are especially evident within the genus Coralliozetus, with different species relationships supported by morphology, TMO-4C4, and RAG1 plus Rhodopsin. This study hypothesizes a novel sistergroup relationship between Ekemblemaria and Hemiemblemaria, consistent with morphological, molecular and habitat use data. Our total evidence phylogenetic hypothesis indicates that previously hypothesized morphological characters supporting a close relationship between Hemiemblemaria and Chaenopsis plus Lucayablennius resulted from convergent evolution in these relatively free-swimming blennies.

  7. Proposal for the New Genus Allokutzneria gen. nov. Within the Suborder Pseudonocardineae and Transfer of Kibdelosporangium albatum Tomita et al. 1993 as Allokutzneria albata comb. nov.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    During the course of phylogenetic analyses based on 16S rRNA gene sequences for all currently described taxa within the family Pseudonocardineae it became evident that Kibdelosporangium albatum DSM 44149T was misplaced within the genus Kibdelosporangium and is phylogenetically most closely related t...

  8. Formation of stylet sheaths in aere (in air) from eight species of phytophagous hemipterans from six families (suborders: Auchenorrhyncha and Sternorrhyncha)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Stylet sheath formation is a common feature among phytophagous hemipterans. These sheaths are considered essential to promote a successful feeding event of these piercing-sucking insects. The stylet sheath composition is unknown, and it is suggested that it forms through interactions with external (...

  9. Formation of Stylet Sheaths in āere (in air) from eight species of phytophagous hemipterans from six families (Suborders: Auchenorrhyncha and Sternorrhyncha).

    PubMed

    Morgan, J Kent; Luzio, Gary A; Ammar, El-Desouky; Hunter, Wayne B; Hall, David G; Shatters, Robert G

    2013-01-01

    Stylet sheath formation is a common feature among phytophagous hemipterans. These sheaths are considered essential to promote a successful feeding event. Stylet sheath compositions are largely unknown and their mode of solidification remains to be elucidated. This report demonstrates the formation and solidification of in āere (in air) produced stylet sheaths by six hemipteran families: Diaphorina citri (Psyllidae, Asian citrus psyllid), Aphis nerii (Aphididae, oleander/milkweed aphid), Toxoptera citricida (Aphididae, brown citrus aphid), Aphis gossypii (Aphididae, cotton melon aphid), Bemisia tabaci biotype B (Aleyrodidae, whitefly), Homalodisca vitripennis (Cicadellidae, glassy-winged sharpshooter), Ferrisia virgata (Pseudococcidae, striped mealybug), and Protopulvinaria pyriformis (Coccidae, pyriform scale). Examination of in āere produced stylet sheaths by confocal and scanning electron microscopy shows a common morphology of an initial flange laid down on the surface of the membrane followed by continuous hollow core structures with sequentially stacked hardened bulbous droplets. Single and multi-branched sheaths were common, whereas mealybug and scale insects typically produced multi-branched sheaths. Micrographs of the in āere formed flanges indicate flange sealing upon stylet bundle extraction in D. citri and the aphids, while the B. tabaci whitefly and H. vitripennis glassy-winged sharpshooter flanges remain unsealed. Structural similarity of in āere sheaths are apparent in stylet sheaths formed in planta, in artificial diets, or in water. The use of 'Solvy', a dissolvable membrane, for intact stylet sheath isolation is reported. These observations illustrate for the first time this mode of stylet sheath synthesis adding to the understanding of stylet sheath formation in phytophagous hemipterans and providing tools for future use in structural and compositional analysis.

  10. Formation of Stylet Sheaths in āere (in air) from Eight Species of Phytophagous Hemipterans from Six Families (Suborders: Auchenorrhyncha and Sternorrhyncha)

    PubMed Central

    Morgan, J. Kent; Luzio, Gary A.; Ammar, El-Desouky; Hunter, Wayne B.; Hall, David G.; Shatters Jr, Robert G.

    2013-01-01

    Stylet sheath formation is a common feature among phytophagous hemipterans. These sheaths are considered essential to promote a successful feeding event. Stylet sheath compositions are largely unknown and their mode of solidification remains to be elucidated. This report demonstrates the formation and solidification of in āere (in air) produced stylet sheaths by six hemipteran families: Diaphorina citri (Psyllidae, Asian citrus psyllid), Aphis nerii (Aphididae, oleander/milkweed aphid), Toxoptera citricida (Aphididae, brown citrus aphid), Aphis gossypii (Aphididae, cotton melon aphid), Bemisia tabaci biotype B (Aleyrodidae, whitefly), Homalodisca vitripennis (Cicadellidae, glassy-winged sharpshooter), Ferrisia virgata (Pseudococcidae, striped mealybug), and Protopulvinaria pyriformis (Coccidae, pyriform scale). Examination of in āere produced stylet sheaths by confocal and scanning electron microscopy shows a common morphology of an initial flange laid down on the surface of the membrane followed by continuous hollow core structures with sequentially stacked hardened bulbous droplets. Single and multi-branched sheaths were common, whereas mealybug and scale insects typically produced multi-branched sheaths. Micrographs of the in āere formed flanges indicate flange sealing upon stylet bundle extraction in D. citri and the aphids, while the B. tabaci whitefly and H. vitripennis glassy-winged sharpshooter flanges remain unsealed. Structural similarity of in āere sheaths are apparent in stylet sheaths formed in planta, in artificial diets, or in water. The use of ‘Solvy’, a dissolvable membrane, for intact stylet sheath isolation is reported. These observations illustrate for the first time this mode of stylet sheath synthesis adding to the understanding of stylet sheath formation in phytophagous hemipterans and providing tools for future use in structural and compositional analysis. PMID:23638086

  11. Enhanced production of antimicrobial compounds by three salt-tolerant actinobacterial strains isolated from the Sundarbans in a niche-mimic bioreactor.

    PubMed

    Sarkar, Sreyashi; Saha, Malay; Roy, Debashis; Jaisankar, Parasuraman; Das, Satadal; Gauri Roy, Lalita; Gachhui, Ratan; Sen, Tuhinadri; Mukherjee, Joydeep

    2008-01-01

    A novel reactor system, the rotating disk bioreactor (RDBR), was used to mimic the niche environmental conditions of three salt-tolerant estuarine actinobacteria isolated from the Sundarbans region off the Bay of Bengal, designated MS310 (99% similar in its 16S rRNA gene sequence to Streptomyces parvallus), MS3/20 and MS1/7. The RDBR, operated at a rotational speed of one revolution per day, 50% submergence of discs, aeration rate of 1.0 vvm, and with a sucrose-containing medium, faithfully mimicked the intertidal estuarine habitat of these marine isolates, and supported biofilm formation and production of antimicrobial metabolites-in particular, actinomycin D by MS310. Onset of antibiotic production by MS310 occurs at 20 h in the RDBR compared to 55 h in a conventional stirred-tank bioreactor (STBR). Furthermore, peak antimicrobial activity is attained much earlier in the RDBR with MS310 (at 45 h) than that reported with a terrestrial strain of S. parvallus grown in a STBR (at 144 h). Peak antimicrobial activity of metabolites produced by MS1/7 and MS3/20 were also attained earlier in the RDBR (at 25 and 12 h, respectively) than in a STBR (at 80 and 28 h, respectively). Antibiotic synthesis in the three isolates, in general, appears to be associated with their growth. Overall, the RDBR may be considered the preferred alternative to the STBR for production of antimicrobials by biofilm-forming estuarine bacteria for its much higher surface/volume ratio, lower costs, and easy operability.

  12. Complete genome sequence of Catenulispora acidiphila type strain (ID 139908T)

    SciTech Connect

    Copeland, A; Lapidus, Alla L.; Glavina Del Rio, Tijana; Nolan, Matt; Lucas, Susan; Chen, Feng; Tice, Hope; Cheng, Jan-Fang; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Mikhailova, Natalia; Pati, Amrita; Ivanova, N; Mavromatis, K; Chen, Amy; Palaniappan, Krishna; Chain, Patrick S. G.; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Chertkov, Olga; Brettin, Thomas S; Detter, J. Chris; Han, Cliff; Ali, Zahid; Tindall, Brian; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2009-01-01

    Catenulispora acidiphila Busti et al. 2006 is the type species of the genus Catenulispora, and is of interest because of the rather isolated phylogenetic location it occupies within the scarcely explored suborder Catenulisporineae of the order Actinomycetales. C. acidiphilia is known for its acidophilic, aerobic lifestyle, but can also grow scantly under anaerobic condi-tions. Under regular conditions, C. acidiphilia grows in long filaments of relatively short aerial hyphae with marked septation. It is a free living, non motile, Gram-positive bacterium iso-lated from a forest soil sample taken from a wooded area in Gerenzano, Italy. Here we de-scribe the features of this organism, together with the complete genome sequence and anno-tation. This is the first complete genome sequence of the actinobacterial family Catenulispo-raceae, and the 10,467,782 bp long single replicon genome with its 9056 protein-coding and 69 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  13. Reassessment of the systematics of the suborder Pseudonocardineae: transfer of the genera within the family Actinosynnemataceae Labeda and Kroppenstedt 2000 emend. Zhi et al. 2009 into an emended family Pseudonocardiaceae...

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The taxonomic status of the families Actinosynnemataceae and Pseudonocardiaceae was assessed based on the 16S rRNA sequence data available for the 152 valid taxa, as well as the chemotaxonomic and morphological properties available from the literature. The 16S rRNA gene sequences for the type strai...

  14. Genus X. Lechevalieria Labeda, Hatano, Kroppenstedt and Tamura 2001, 1049vp

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The physiology, systematics and ecology of the species that currently compose the actinobacterial genus Lechevalieria is presented. The phylogenetic position of the taxa within this genus, including Lecehvalieria aerocolonigenes, Lechevalieria flava, Lechevalieria fradiae, and Lechevalieria xinjian...

  15. Genus VIII. Kibdelosporangium Shearer, Colman, Ferrin, Nisbet and Nash 1986, 48

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The morphology, physiology, systematics, ecology, and natural products of the species that currently compose the actinobacterial genus Kibdelosporangium is presented. The phylogenetic position of the taxa within this genus, including Kibdelosporangium aridum subsp. aridum, Kibdelosporangium aridum ...

  16. Genus XI. Lentzea Yassin, Rainey, Brzezinka, Jahnke, Weissbrodt, Budzikiewicz, Stackebrandt, and Schaal 1995, 362vp emend. Labeda, Hatano, Kroppenstedt and Tamura 2001, 1049

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The physiology, systematics and ecology of the species that currently compose the actinobacterial genus Lentzea is presented. The phylogenetic position of the taxa within this genus, including Lentzea albidocapillata, Lentzea albida, Lentzea californiensis, Lentzea flaviverrucosa, Lentzea kentuckye...

  17. Genus Goodfellowiella (Labeda and Kroppenstedt 2006) Labeda, Kroppenstedt, Euzeby and Tindall 2008, 1048vp

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The physiology, systematics and ecology of the species that currently composes the actinobacterial genus Goodfellowiella is presented. The phylogenetic position of the lone species within this genus, Goodfellowiella coeruleoviolacea relative to the other genera within the family Pseudonocardinaea i...

  18. Genus XV. Saccharothrix Labeda, Testa, Lechevalier and Lechevalier 1984, 429vp emend. Labeda and Lechevalier 1989, 422

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The physiology, systematics, ecology, and natural products of the species that currently compose the actinobacterial genus Saccharothrix is presented. The phylogenetic position of the taxa within this genus, including Saccharothrix algeriensis, Saccharothrix australiensis, Saccharothrix coeruleofla...

  19. Surfactants tailored by the class Actinobacteria

    PubMed Central

    Kügler, Johannes H.; Le Roes-Hill, Marilize; Syldatk, Christoph; Hausmann, Rudolf

    2015-01-01

    Globally the change towards the establishment of a bio-based economy has resulted in an increased need for bio-based applications. This, in turn, has served as a driving force for the discovery and application of novel biosurfactants. The class Actinobacteria represents a vast group of microorganisms with the ability to produce a diverse range of secondary metabolites, including surfactants. Understanding the extensive nature of the biosurfactants produced by actinobacterial strains can assist in finding novel biosurfactants with new potential applications. This review therefore presents a comprehensive overview of the knowledge available on actinobacterial surfactants, the chemical structures that have been completely or partly elucidated, as well as the identity of the biosurfactant-producing strains. Producer strains of not yet elucidated compounds are discussed, as well as the original habitats of all the producer strains, which seems to indicate that biosurfactant production is environmentally driven. Methodology applied in the isolation, purification and structural elucidation of the different types of surface active compounds, as well as surfactant activity tests, are also discussed. Overall, actinobacterial surfactants can be summarized to include the dominantly occurring trehalose-comprising surfactants, other non-trehalose containing glycolipids, lipopeptides and the more rare actinobacterial surfactants. The lack of structural information on a large proportion of actinobacterial surfactants should be considered as a driving force to further explore the abundance and diversity of these compounds. This would allow for a better understanding of actinobacterial surface active compounds and their potential for biotechnological application. PMID:25852670

  20. Ruminant feces harbor diverse uncultured symbiotic actinobacteria.

    PubMed

    Tan, Hongming; Deng, Qingli; Cao, Lixiang

    2014-03-01

    To isolate actinobacteria from ruminant feces and elucidate their correlations with ruminants, the actinobacterial community in sheep (Ovis aries) and cattle (Bos taurus) feces was determined by cultivation and clone library methods. Most of actinobacteria isolated belonged to Streptomyces, Amycolatopsis, Micromonospora, and Cellulosimicrobium genera. The strains showed above 99 % similarity with the type strains, respectively. All the strains isolated could grow on media containing pectin, cellulose, or xylan as the sole carbon sources. However, most antibacterial and antifungal activities were found in Streptomyces species. Clone library analysis revealed that the genera Mycobacterium, Aeromicrobium, Rhodococcus, Cellulomonas were present in cattle and sheep feces. In contrast, the 16S rRNA genes showed less than 98 % similarity with the type strains. The analysis of actinobacterial community in ruminant feces by clone library and cultivation yielded a total of 10 actinobacterial genera and three uncultured actinobacterial taxa. The ruminant feces harbored diverse actinobacterial community. Ruminants may represent an underexplored reservoir of novel actinomycetes of potential interest for probiotics and drug discovery.

  1. Land Leeches of the g. Haemadipsa (Haemadipsoidea: Haemadipsidae). I. Conditions Essential to Laboratory Colonization.

    DTIC Science & Technology

    1982-05-01

    segmented aquatic and terrestrial worms that belong to the Order Hirudinea, ( Annelida : Clitellata, Scriban and Autrum (2)) and are most closely related to the...WORTH, C.B. Description and discussion of the biting of an Indian land leech. ( Annelida : Hirudinea). J Bombay Nat Hist Soc 50:423-426, 1951 39...Haemadlpsidae and their Suborder, the Gnathobdellae (after 2-6,60). Phylum: Annelida Class: Clitellata Order: Ifirudinea (=Hirudiniformes) Suborder 1

  2. Antimicrobial Screening of Actinobacteria using a Modified Cross-Streak Method

    PubMed Central

    Velho-Pereira, Sonashia; Kamat, N M

    2011-01-01

    Out of the 30 actinobacterial cultures screened for antimicrobial activity, 28 cultures were found to produce active products against various pathogenic microorganisms such as Gram-negative, Gram-positive bacteria and yeast, using a modified cross streak method. The modified method helped in easy quantification of results and also in ruling out probable mutual antibiosis. The actinobacterial strains that showed the ability to produce antimicrobial compounds belonged to Streptomyces (53%), Micromonospora (13%) and Actinomadura (10%) genera. Streptomyces sp. strain MMA-5 showed the highest multispecific antibiosis efficiency score value. Broad antibiotic spectrum activity was exhibited by Streptomyces sp. strain MMA-2 and Micromonospora sp. strain MMA-8. The multidrug resistant human pathogenic yeast strain Candida albicans was inhibited by 18 actinobacterial strains. PMID:22303068

  3. Diversity, Biogeography, and Biodegradation Potential of Actinobacteria in the Deep-Sea Sediments along the Southwest Indian Ridge

    PubMed Central

    Chen, Ping; Zhang, Limin; Guo, Xiaoxuan; Dai, Xin; Liu, Li; Xi, Lijun; Wang, Jian; Song, Lei; Wang, Yuezhu; Zhu, Yaxin; Huang, Li; Huang, Ying

    2016-01-01

    The phylum Actinobacteria has been reported to be common or even abundant in deep marine sediments, however, knowledge about the diversity, distribution, and function of actinobacteria is limited. In this study, actinobacterial diversity in the deep sea along the Southwest Indian Ridge (SWIR) was investigated using both 16S rRNA gene pyrosequencing and culture-based methods. The samples were collected at depths of 1662–4000 m below water surface. Actinobacterial sequences represented 1.2–9.1% of all microbial 16S rRNA gene amplicon sequences in each sample. A total of 5 actinobacterial classes, 17 orders, 28 families, and 52 genera were detected by pyrosequencing, dominated by the classes Acidimicrobiia and Actinobacteria. Differences in actinobacterial community compositions were found among the samples. The community structure showed significant correlations to geochemical factors, notably pH, calcium, total organic carbon, total phosphorus, and total nitrogen, rather than to spatial distance at the scale of the investigation. In addition, 176 strains of the Actinobacteria class, belonging to 9 known orders, 18 families, and 29 genera, were isolated. Among these cultivated taxa, 8 orders, 13 families, and 15 genera were also recovered by pyrosequencing. At a 97% 16S rRNA gene sequence similarity, the pyrosequencing data encompassed 77.3% of the isolates but the isolates represented only 10.3% of the actinobacterial reads. Phylogenetic analysis of all the representative actinobacterial sequences and isolates indicated that at least four new orders within the phylum Actinobacteria were detected by pyrosequencing. More than half of the isolates spanning 23 genera and all samples demonstrated activity in the degradation of refractory organics, including polycyclic aromatic hydrocarbons and polysaccharides, suggesting their potential ecological functions and biotechnological applications for carbon recycling. PMID:27621725

  4. Diversity, Biogeography, and Biodegradation Potential of Actinobacteria in the Deep-Sea Sediments along the Southwest Indian Ridge.

    PubMed

    Chen, Ping; Zhang, Limin; Guo, Xiaoxuan; Dai, Xin; Liu, Li; Xi, Lijun; Wang, Jian; Song, Lei; Wang, Yuezhu; Zhu, Yaxin; Huang, Li; Huang, Ying

    2016-01-01

    The phylum Actinobacteria has been reported to be common or even abundant in deep marine sediments, however, knowledge about the diversity, distribution, and function of actinobacteria is limited. In this study, actinobacterial diversity in the deep sea along the Southwest Indian Ridge (SWIR) was investigated using both 16S rRNA gene pyrosequencing and culture-based methods. The samples were collected at depths of 1662-4000 m below water surface. Actinobacterial sequences represented 1.2-9.1% of all microbial 16S rRNA gene amplicon sequences in each sample. A total of 5 actinobacterial classes, 17 orders, 28 families, and 52 genera were detected by pyrosequencing, dominated by the classes Acidimicrobiia and Actinobacteria. Differences in actinobacterial community compositions were found among the samples. The community structure showed significant correlations to geochemical factors, notably pH, calcium, total organic carbon, total phosphorus, and total nitrogen, rather than to spatial distance at the scale of the investigation. In addition, 176 strains of the Actinobacteria class, belonging to 9 known orders, 18 families, and 29 genera, were isolated. Among these cultivated taxa, 8 orders, 13 families, and 15 genera were also recovered by pyrosequencing. At a 97% 16S rRNA gene sequence similarity, the pyrosequencing data encompassed 77.3% of the isolates but the isolates represented only 10.3% of the actinobacterial reads. Phylogenetic analysis of all the representative actinobacterial sequences and isolates indicated that at least four new orders within the phylum Actinobacteria were detected by pyrosequencing. More than half of the isolates spanning 23 genera and all samples demonstrated activity in the degradation of refractory organics, including polycyclic aromatic hydrocarbons and polysaccharides, suggesting their potential ecological functions and biotechnological applications for carbon recycling.

  5. Hidden among sea anemones: the first comprehensive phylogenetic reconstruction of the order Actiniaria (Cnidaria, Anthozoa, Hexacorallia) reveals a novel group of hexacorals.

    PubMed

    Rodríguez, Estefanía; Barbeitos, Marcos S; Brugler, Mercer R; Crowley, Louise M; Grajales, Alejandro; Gusmão, Luciana; Häussermann, Verena; Reft, Abigail; Daly, Marymegan

    2014-01-01

    Sea anemones (order Actiniaria) are among the most diverse and successful members of the anthozoan subclass Hexacorallia, occupying benthic marine habitats across all depths and latitudes. Actiniaria comprises approximately 1,200 species of solitary and skeleton-less polyps and lacks any anatomical synapomorphy. Although monophyly is anticipated based on higher-level molecular phylogenies of Cnidaria, to date, monophyly has not been explicitly tested and at least some hypotheses on the diversification of Hexacorallia have suggested that actiniarians are para- or poly-phyletic. Published phylogenies have demonstrated the inadequacy of existing morphological-based classifications within Actiniaria. Superfamilial groups and most families and genera that have been rigorously studied are not monophyletic, indicating conflict with the current hierarchical classification. We test the monophyly of Actiniaria using two nuclear and three mitochondrial genes with multiple analytical methods. These analyses are the first to include representatives of all three currently-recognized suborders within Actiniaria. We do not recover Actiniaria as a monophyletic clade: the deep-sea anemone Boloceroides daphneae, previously included within the infraorder Boloceroidaria, is resolved outside of Actiniaria in several of the analyses. We erect a new genus and family for B. daphneae, and rank this taxon incerti ordinis. Based on our comprehensive phylogeny, we propose a new formal higher-level classification for Actiniaria composed of only two suborders, Anenthemonae and Enthemonae. Suborder Anenthemonae includes actiniarians with a unique arrangement of mesenteries (members of Edwardsiidae and former suborder Endocoelantheae). Suborder Enthemonae includes actiniarians with the typical arrangement of mesenteries for actiniarians (members of former suborders Protantheae, Ptychodacteae, and Nynantheae and subgroups therein). We also erect subgroups within these two newly-erected suborders

  6. Coral-Associated Actinobacteria: Diversity, Abundance, and Biotechnological Potentials

    PubMed Central

    Mahmoud, Huda M.; Kalendar, Aisha A.

    2016-01-01

    Marine Actinobacteria, particularly coral-associated Actinobacteria, have attracted attention recently. In this study, the abundance and diversity of Actinobacteria associated with three types of coral thriving in a thermally stressed coral reef system north of the Arabian Gulf were investigated. Coscinaraea columna, Platygyra daedalea and Porites harrisoni have been found to harbor equivalent numbers of culturable Actinobacteria in their tissues but not in their mucus. However, different culturable actinobacterial communities have been found to be associated with different coral hosts. Differences in the abundance and diversity of Actinobacteria were detected between the mucus and tissue of the same coral host. In addition, temporal and spatial variations in the abundance and diversity of the cultivable actinobacterial communities were detected. In total, 19 different actinobacterial genera, namely Micrococcus, Brachybacterium, Brevibacterium, Streptomyces, Micromonospora, Renibacterium, Nocardia, Microbacterium, Dietzia, Cellulomonas, Ornithinimicrobium, Rhodococcus, Agrococcus, Kineococcus, Dermacoccus, Devriesea, Kocuria, Marmoricola, and Arthrobacter, were isolated from the coral tissue and mucus samples. Furthermore, 82 isolates related to Micromonospora, Brachybacterium, Nocardia, Micrococcus, Arthrobacter, Rhodococcus, and Streptomyces showed antimicrobial activities against representative Gram-positive and/or Gram-negative bacteria. Even though Brevibacterium and Kocuria were the most dominant actinobacterial isolates, they failed to show any antimicrobial activity, whereas less dominant genera, such as Streptomyces, did show antimicrobial activity. Focusing on the diversity of coral-associated Actinobacteria may help to understand how corals thrive under harsh environmental conditions and may lead to the discovery of novel antimicrobial metabolites with potential biotechnological applications. PMID:26973601

  7. Biogeography of bacterial communities in hot springs: a focus on the actinobacteria.

    PubMed

    Valverde, Angel; Tuffin, Marla; Cowan, Don A

    2012-07-01

    Actinobacteria are ubiquitous in soil, freshwater and marine ecosystems. Although various studies have focused on the microbial ecology of this phylum, data are scant on the ecology of actinobacteria endemic to hot springs. Here, we have investigated the molecular diversity of eubacteria, with specific focus on the actinobacteria in hot springs in Zambia, China, New Zealand and Kenya. Temperature and pH values at sampling sites ranged between 44.5 and 86.5 °C and 5-10, respectively. Non-metric multidimensional scaling analysis of 16S rRNA gene T-RFLP patterns showed that samples could be separated by geographical location. Multivariate analysis showed that actinobacterial community composition was best predicted by changes in pH and temperature, whereas temperature alone was the most important variable explaining differences in bacterial community structure. Using 16S rRNA gene libraries, 28 major actinobacterial OTUs were found. Both molecular techniques indicated that many of the actinobacterial phylotypes were unique and exclusive to the respective sample. Collectively, these results support the view that both actinobacterial diversity and endemism are high in hot spring ecosystems.

  8. Draft Genome Sequence of Dietzia alimentaria 72T, Belonging to the Family Dietziaceae, Isolated from a Traditional Korean Food

    PubMed Central

    Kim, Jandi; Roh, Seong Woon; Bae, Jin-Woo

    2011-01-01

    Actinobacterial strain 72T, named Dietzia alimentaria, which belongs to the family Dietziaceae, was isolated from a traditional Korean food made from clams. The draft genome sequence of D. alimentaria 72T contains 3,352,817 bp, with a G+C content of 67.34%. PMID:22072646

  9. Genus IV. Actinosynnema Hasegawa, Lechevalier and Lechevalier 1978, 304al

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The physiology, systematics and ecology of the species that currently composes the actinobacterial genus Actinosynnema is presented. The phylogenetic position of the species within this genus relative to the other genera within the family Actinosynnemataceae is discussed. Methods for isolation, pr...

  10. Coral-Associated Actinobacteria: Diversity, Abundance, and Biotechnological Potentials.

    PubMed

    Mahmoud, Huda M; Kalendar, Aisha A

    2016-01-01

    Marine Actinobacteria, particularly coral-associated Actinobacteria, have attracted attention recently. In this study, the abundance and diversity of Actinobacteria associated with three types of coral thriving in a thermally stressed coral reef system north of the Arabian Gulf were investigated. Coscinaraea columna, Platygyra daedalea and Porites harrisoni have been found to harbor equivalent numbers of culturable Actinobacteria in their tissues but not in their mucus. However, different culturable actinobacterial communities have been found to be associated with different coral hosts. Differences in the abundance and diversity of Actinobacteria were detected between the mucus and tissue of the same coral host. In addition, temporal and spatial variations in the abundance and diversity of the cultivable actinobacterial communities were detected. In total, 19 different actinobacterial genera, namely Micrococcus, Brachybacterium, Brevibacterium, Streptomyces, Micromonospora, Renibacterium, Nocardia, Microbacterium, Dietzia, Cellulomonas, Ornithinimicrobium, Rhodococcus, Agrococcus, Kineococcus, Dermacoccus, Devriesea, Kocuria, Marmoricola, and Arthrobacter, were isolated from the coral tissue and mucus samples. Furthermore, 82 isolates related to Micromonospora, Brachybacterium, Nocardia, Micrococcus, Arthrobacter, Rhodococcus, and Streptomyces showed antimicrobial activities against representative Gram-positive and/or Gram-negative bacteria. Even though Brevibacterium and Kocuria were the most dominant actinobacterial isolates, they failed to show any antimicrobial activity, whereas less dominant genera, such as Streptomyces, did show antimicrobial activity. Focusing on the diversity of coral-associated Actinobacteria may help to understand how corals thrive under harsh environmental conditions and may lead to the discovery of novel antimicrobial metabolites with potential biotechnological applications.

  11. Genus XIII. Umezawaea Labeda and Kroppenstedt 2007, 2761vp

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The physiology, systematics and ecology of the species that currently compose the actinobacterial genus Umezawaea is presented. The phylogenetic position of the lone species within this genus, Umezawaea tangerina relative to the species in other genera within the family Actinosynnemataceae is discu...

  12. Dispersal limitation and the assembly of soil Actinobacteria communities in a long-term chronosequence

    PubMed Central

    Eisenlord, Sarah D; Zak, Donald R; Upchurch, Rima A

    2012-01-01

    It is uncertain whether the same ecological forces that structure plant and animal communities also shape microbial communities, especially those residing in soil. We sought to uncover the relative importance of present-day environmental characteristics, climatic variation, and historical contingencies in shaping soil actinobacterial communities in a long-term chronosequence. Actinobacteria communities were characterized in surface soil samples from four replicate forest stands with nearly identical edaphic and ecological properties, which range from 9500 to 14,000 years following glacial retreat in Michigan. Terminal restriction fragment length polymorphism (TRFLP) profiles and clone libraries of the actinobacterial 16S rRNA gene were constructed in each site for phenetic and phylogenetic analysis to determine whether dispersal limitation occurred following glacial retreat, or if community composition was determined by environmental heterogeneity. At every level of examination, actinobacterial community composition most closely correlated with distance, a surrogate for time, than with biogeochemical, plant community, or climatic characteristics. Despite correlation with leaf litter C:N and annual temperature, the significant and consistent relationship of biological communities with time since glacial retreat provides evidence that dispersal limitation is an ecological force structuring actinobacterial communities in soil over long periods of time. PMID:22822433

  13. Complete Genome Sequence of Kocuria palustris MU14/1

    PubMed Central

    Foecking, Mark F.

    2015-01-01

    Presented here is the first completely assembled genome sequence of Kocuria palustris, an actinobacterial species with broad ecological distribution. The single, circular chromosome of K. palustris MU14/1 comprises 2,854,447 bp, has a G+C content of 70.5%, and contains a deduced gene set of 2,521 coding sequences. PMID:26472837

  14. Potential for biocontrol of melanized fungi by actinobacteria isolated from intertidal region of Ilha Do Mel, Paraná, Brazil.

    PubMed

    Dalitz, Camila de Araújo; Porsani, Mariana Vieira; Figel, Izabel Cristina; Pimentel, Ida C; Dalzoto, Patrícia R

    Actinobacteria occur in many environments and have the capacity to produce secondary metabolites with antibiotic potential. Identification and taxonomy of actinobacteria that produce antimicrobial substances is essential for the screening of new compounds, and sequencing of the 16S region of ribosomal DNA (rDNA), which is conserved and present in all bacteria, is an important method of identification. Melanized fungi are free-living organisms, which can also be pathogens of clinical importance. This work aimed to evaluate growth inhibition of melanized fungi by actinobacteria and to identify the latter to the species level. In this study, antimicrobial activity of 13 actinobacterial isolates from the genus Streptomyces was evaluated against seven melanized fungi of the genera Exophiala, Cladosporium, and Rhinocladiella. In all tests, all actinobacterial isolates showed inhibitory activity against all isolates of melanized fungi, and only one actinobacterial isolate had less efficient inhibitory activity. The 16S rDNA region of five previously unidentified actinobacterial isolates from Ilha do Mel, Paraná, Brazil, was sequenced; four of the isolates were identified as Streptomyces globisporus subsp. globisporus, and one isolate was identified as Streptomyces aureus. This work highlights the potential of actinobacteria with antifungal activity and their role in the pursuit of novel antimicrobial substances.

  15. Family I. Pseudonocardiaceae Embley, Smida, and Stackebrandt 1989, 205vp emend. Labeda, Goodfellow, Chun, Zhi and Li 2010a

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The formal description of the actinobacterial higher taxon the family Pseudonocardiaceae is presented. The differential morphological and chemotaxonomic characteristics and diagnostic signature nucleotides from the 16S rRNA gene for the genera in the family is discussed. A key to the identificatio...

  16. Environmental Controls Over Actinobacteria Communities in Ecological Sensitive Yanshan Mountains Zone

    PubMed Central

    Tang, Hui; Shi, Xunxun; Wang, Xiaofei; Hao, Huanhuan; Zhang, Xiu-Min; Zhang, Li-Ping

    2016-01-01

    The Yanshan Mountains are one of the oldest mountain ranges in the world. They are located in an ecologically sensitive zone in northern China near the Hu Huanyong Line. In this metagenomic study, we investigated the diversity of Actinobacteria in soils at 10 sites (YS1–YS10) on the Yanshan Mountains. First, we assessed the effect of different soil prtreatment on Actinobacteria recovery. With the soil pretreatment method: air drying of the soil sample, followed by exposure to 120°C for 1 h, we observed the higher Actinobacteria diversity in a relatively small number of clone libraries. No significant differences were observed in the Actinobacterial diversity of soils from sites YS2, YS3, YS4, YS6, YS8, YS9, or YS10 (P > 0.1). However, there were differences (P < 0.05) from the YS7 site and other sites, especially in response to environmental change. And we observed highly significant differences (P < 0.001) in Actinobacterial diversity of the soil from YS7 and that from YS4 and YS8 sites. The climatic characteristics of mean active accumulated temperature, annual mean precipitation, and annual mean temperature, and biogeochemical data of total phosphorus contributed to the diversity of Actinobacterial communities in soils at YS1, YS3, YS4, and YS5 sites. Compared to the climatic factors, the biogeochemical factors mostly contributed in shaping the Actinobacterial community. This work provides evidence that the diversity of Actinobacterial communities in soils from the Yashan Mountains show regional biogeographic patterns and that community membership change along the north-south distribution of the Hu Huanyong Line. PMID:27047461

  17. Rational approaches to improving the isolation of endophytic actinobacteria from Australian native trees.

    PubMed

    Kaewkla, Onuma; Franco, Christopher M M

    2013-02-01

    In recent years, new actinobacterial species have been isolated as endophytes of plants and shrubs and are sought after both for their role as potential producers of new drug candidates for the pharmaceutical industry and as biocontrol inoculants for sustainable agriculture. Molecular-based approaches to the study of microbial ecology generally reveal a broader microbial diversity than can be obtained by cultivation methods. This study aimed to improve the success of isolating individual members of the actinobacterial population as pure cultures as well as improving the ability to characterise the large numbers obtained in pure culture. To achieve this objective, our study successfully employed rational and holistic approaches including the use of isolation media with low concentrations of nutrients normally available to the microorganism in the plant, plating larger quantities of plant sample, incubating isolation plates for up to 16 weeks, excising colonies when they are visible and choosing Australian endemic trees as the source of the actinobacteria. A hierarchy of polyphasic methods based on culture morphology, amplified 16S rRNA gene restriction analysis and limited sequencing was used to classify all 576 actinobacterial isolates from leaf, stem and root samples of two eucalypts: a Grey Box and Red Gum, a native apricot tree and a native pine tree. The classification revealed that, in addition to 413 Streptomyces spp., isolates belonged to 16 other actinobacterial genera: Actinomadura (two strains), Actinomycetospora (six), Actinopolymorpha (two), Amycolatopsis (six), Gordonia (one), Kribbella (25), Micromonospora (six), Nocardia (ten), Nocardioides (11), Nocardiopsis (one), Nonomuraea (one), Polymorphospora (two), Promicromonospora (51), Pseudonocardia (36), Williamsia (two) and a novel genus Flindersiella (one). In order to prove novelty, 12 strains were characterised fully to the species level based on polyphasic taxonomy. One strain represented a novel

  18. Environmental Controls Over Actinobacteria Communities in Ecological Sensitive Yanshan Mountains Zone.

    PubMed

    Tang, Hui; Shi, Xunxun; Wang, Xiaofei; Hao, Huanhuan; Zhang, Xiu-Min; Zhang, Li-Ping

    2016-01-01

    The Yanshan Mountains are one of the oldest mountain ranges in the world. They are located in an ecologically sensitive zone in northern China near the Hu Huanyong Line. In this metagenomic study, we investigated the diversity of Actinobacteria in soils at 10 sites (YS1-YS10) on the Yanshan Mountains. First, we assessed the effect of different soil prtreatment on Actinobacteria recovery. With the soil pretreatment method: air drying of the soil sample, followed by exposure to 120°C for 1 h, we observed the higher Actinobacteria diversity in a relatively small number of clone libraries. No significant differences were observed in the Actinobacterial diversity of soils from sites YS2, YS3, YS4, YS6, YS8, YS9, or YS10 (P > 0.1). However, there were differences (P < 0.05) from the YS7 site and other sites, especially in response to environmental change. And we observed highly significant differences (P < 0.001) in Actinobacterial diversity of the soil from YS7 and that from YS4 and YS8 sites. The climatic characteristics of mean active accumulated temperature, annual mean precipitation, and annual mean temperature, and biogeochemical data of total phosphorus contributed to the diversity of Actinobacterial communities in soils at YS1, YS3, YS4, and YS5 sites. Compared to the climatic factors, the biogeochemical factors mostly contributed in shaping the Actinobacterial community. This work provides evidence that the diversity of Actinobacterial communities in soils from the Yashan Mountains show regional biogeographic patterns and that community membership change along the north-south distribution of the Hu Huanyong Line.

  19. Multiple origins of parasitism in lice: phylogenetic analysis of SSU rDNA indicates that the Phthiraptera and Psocoptera are not monophyletic.

    PubMed

    Murrell, Anna; Barker, Stephen C

    2005-10-01

    The Paraneoptera (Hemipteroid Assemblage) comprises the orders Thysanoptera (thrips), Hemiptera (bugs), Phthiraptera (lice) and Psocoptera (booklice and barklice). The phylogenetic relationships among the Psocodea (Phthiraptera and Psocoptera), Thysanoptera and Hemiptera are unresolved, as are some relationships within the Psocodea. Here, we present phylogenetic hypotheses inferred from SSU rDNA sequences; the most controversial of which is the apparent paraphyly of the Phthiraptera, which are parasites of birds and mammals, with respect to one family of Psocoptera, the Liposcelididae. The order Psocoptera and the suborder that contains the Liposcelididae, the Troctomorpha, are also paraphyletic. The two remaining psocopteran suborders, the Psocomorpha and the Trogiomorpha, are apparently monophyletic. The Liposcelididae is most closely related to lice from the suborder Amblycera. These results suggest that the taxonomy of the Psocodea needs revision. In addition, there are implications for the evolution of parasitism in insects; parasitism may have evolved twice in lice or have evolved once and been subsequently lost in the Liposcelididae.

  20. Little known chewing lice (Phthiraptera) infesting crab plover Dromas ardeola Paykull, 1805 (Charadriiformes: Dromadidae) from the Red Sea.

    PubMed

    Alahmed, Azzam; Shobrak, Mohammed; Kheir, Salah; Nasser, Mohamed

    2015-10-01

    Scanty information is available for many species of chewing lice of marine birds. Through this work we investigated one of most characteristic marine bird for chewing lice. Seven individuals of crab plovers Dromas ardeola Paykull, 1805 were trapped using standard mist nets on Humr Island in Farasan Archipelago, Saudi Arabia. Two species of chewing lice were found to infest these birds: Actornithophilus ardeolae Timmermann, 1954 of suborder Amblycera and Quadraceps brunneus (Nitzsch in Giebel, 1866) of suborder Ischnocera. Diagnostic characters, data of specimens examined, high definition photos and host distribution map are provided through this paper.

  1. First records of the chewing lice (Phthiraptera) associated with European bee eater (Merops apiaster) in Saudi.

    PubMed

    El-Ahmed, Azzam; Gamal, El-Den Nasser Mohammed; Shobrak, Mohamed; Dik, Bilal

    2012-12-01

    The European bee-eater (Merops apiaster) migrates through Saudi Arabia annually. A total of 25 individuals of this species were captured from three localities in Riyadh and Ta'if. Three species of chewing lice were identified from these birds and newly added to list of Saudi Arabia parasitic lice fauna from 160 lice individuals, Meromenopon meropis of suborder Amblycera, Brueelia apiastri and Meropoecus meropis of suborder Ischnocera. The characteristic feature, identification keys, data on the material examined, synonyms, photo, type and type locality are provide to each species.

  2. Extraordinary number of gene rearrangements in the mitochondrial genomes of lice (Phthiraptera: Insecta).

    PubMed

    Covacin, C; Shao, R; Cameron, S; Barker, S C

    2006-02-01

    The arrangement of genes in the mitochondrial (mt) genomes of most insects is the same, or near-identical, to that inferred to be ancestral for insects. We sequenced the entire mt genome of the small pigeon louse, Campanulotes bidentatus compar, and part of the mt genomes of nine other species of lice. These species were from six families and the three main suborders of the order Phthiraptera. There was no variation in gene arrangement among species within a family but there was much variation in gene arrangement among the three suborders of lice. There has been an extraordinary number of gene rearrangements in the mitochondrial genomes of lice!

  3. Detection of a novel gammaherpesvirus in koalas (Phascolarctos cinereus).

    PubMed

    Vaz, P; Whiteley, P L; Wilks, C R; Duignan, P J; Ficorilli, N; Gilkerson, J R; Browning, G F; Devlin, J M

    2011-07-01

    A novel gammaherpesvirus was detected in wild koalas (Phascolarctos cinereus) captured at different locations during 2010. Sequence analysis of the DNA polymerase gene revealed that the virus was genetically distinct from all known gammaherpesviruses. This is the first herpesvirus to be definitively identified in the Vombatiforme suborder (koalas and wombats).

  4. MOLECULAR PHYLOGENY OF LARGE MILIOLID FORAMINIFERA. (R825869)

    EPA Science Inventory

    Abstract

    The foraminiferal superfamily Soritacea belongs to the suborder Miliolina and is divided in two families, Peneroplidae and Soritidae, the latter one comprising two subfamilies, Archaiasinae and Soritinae. Phylogenetic relationships of 11 genera of soritid fora...

  5. Shape as a Facilitating Factor of Changes in Foraminiferan Shell Size

    NASA Astrophysics Data System (ADS)

    Zalles, L.; Seixas, G.; Payne, J.

    2012-12-01

    Some questions remain regarding the factors facilitating changes in body size of marine organisms over geological time. One such possible factor is body shape, which is intrinsically linked to size. By identifying patterns in shape, we hope to gain a better understanding of how changes in shape facilitate changes in size. For example, we can examine whether an increase in the size of an organism must be accommodated by a change in shape. As such, shape has the potential to be used as a predictor for an organism's success at various body sizes. To identify test (i.e., shell) shape patterns, we measured size dimensions of foraminifera, single-celled marine organisms, from the Ellis and Messina Catalogue of Foraminifera. We quantified shape as the ratio between each foraminifer's largest and smallest dimension (dimension ratio). We then compared shape to average body volume over time, looking at five major foraminifera suborders individually as well as combined data for all suborders. We found that while the maximum dimension ratio tends to increase over time, the average remains relatively constant. This trend is apparent in most examined suborders but is less clear in the suborder Fusilinina. When shape was compared to average volume over time, a similar positive correlation was observed. As maximum dimension ratio increases, average volume also increases; this tendency for foraminifera to become less spherical at larger size may reflect constraints related to food and nutrient uptake, supporting the conclusion that shape acts as a facilitating factor in changes in body size of foraminifera.

  6. Thysanoptera-Terebrantia of the Hawaiian Islands: an identification manual

    PubMed Central

    Mound, Laurence; Nakahara, Sueo; Tsuda, Dick M.

    2016-01-01

    Abstract An illustrated identification system is presented to 99 species and 49 genera in three families recorded from the Hawaiian Islands in the Thysanoptera suborder Terebrantia. Only seven (possibly eight) of these species are considered endemic, the remainder being adventive to these islands. The only previous study of Hawaiian Thysanoptera, by Zimmerman in 1948, included 47 Terebrantia species in 21 genera. PMID:26843832

  7. Phylogenetic relationships among families of Gadiformes (Teleostei, Paracanthopterygii) based on nuclear and mitochondrial data.

    PubMed

    Roa-Varón, Adela; Ortí, Guillermo

    2009-09-01

    Phylogenetic hypotheses among Gadiformes fishes at the suborder, family, and subfamily levels are controversial. To address this problem, we analyze nuclear and mitochondrial DNA (mtDNA) sequences for the most extensive taxonomic sampling compiled to date, representing all of the recognized families and subfamilies in the order (except the monotypic family Lyconidae). Our study sampled 117 species from 46 genera, comprising around 20% of the species described for the order (more than 60% of all genera in the order) and produced 2740 bp of DNA sequence data for each species. Our analysis was successful in confirming the monophyly of Gadiformes and most of the proposed families for the order, but alternative hypotheses of sister-group relationships among families were poorly resolved. Our results are consistent with dividing Gadiformes into 12 families in three suborders, Muraenolepidoidei, Macrouroidei, and Gadoidei. Muraenolepidoidei contains the single family Muraenolepididae. The suborder Macrouroidei includes at least three families: Macrouridae, Macruronidae and Steindachneriidae. Macrouridae is deeply divided into two well-supported subfamilies: Macrourinae and Bathygadinae, suggesting that Bathygadinae may be ranked at the family level. The suborder Gadoidei includes the families: Merlucciidae, Melanonidae, Euclichthyidae, Gadidae, Ranicipitidae, and Bregmacerotidae. Additionally, Trachyrincinae could be ranked at family level including two subfamilies: Trachyrincinae and Macrouroidinae within Gadoidei. Further taxonomic sampling and sequencing efforts are needed in order to corroborate these relationships.

  8. No Latitudinal Trends in Body Size of Foraminifera

    NASA Astrophysics Data System (ADS)

    Liao, Z.; Payne, J.; Seixas, G.

    2012-12-01

    Many organisms, such as penguins and polar bears, follow Bergmann's rule, which states that body size of animals tends to increase as temperature decreases, and thus as latitude increases toward to poles. A study of marine mollusk bivalves across a latitudinal gradient found no correlation between body size and latitude along the North American Pacific Coast, suggesting that the body size of marine bivalves might be controlled by other factors. This posed the question: Is there a lack of correlation between latitude and body size for all marine invertebrates or is it unique to marine bivalves? In this study, we examined four suborders of benthic foraminifera, Lagenina, Miliolina, Rotaliina, and Textulariina, a diverse phylum of amoeboid protists, to determine the relationship between body size and latitude within and across suborders at the global scale. We measured the shell (test) dimensions of foraminifera from a compilation of monograph images of type specimens. The mean test size as well as the maximum body size of those foraminifera suborders does not vary with increasing latitude. Our results show that foraminifera do not follow Bergmann's rule, consistent with the body size distribution pattern observed in marine bivalves. Different biological and environmental factors that vary between foraminifera suborders, such as life habitats, behaviors, and physiology, might have a greater influence on body size distributions.

  9. Soil Genesis and Development, Lesson 5 - Soil Geography and Classification

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The system of soil classification developed by the United States Department of Agriculture (USDA) is called Soil Taxonomy. Soil Taxonomy consists of a hierarchy of six levels which, from highest to lowest, are: Order, Suborder, Great Group, Subgroup, family, and series. This lesson will focus on bro...

  10. Complete genome sequence of Cellulomonas flavigena type strain (134T)

    SciTech Connect

    Abt, Birte; Foster, Brian; Lapidus, Alla L.; Clum, Alicia; Sun, Hui; Pukall, Rudiger; Lucas, Susan; Glavina Del Rio, Tijana; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Ivanova, N; Mavromatis, K; Ovchinnikova, Galina; Pati, Amrita; Goodwin, Lynne A.; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Rohde, Manfred; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-01-01

    Cellulomonas flavigena (Kellerman and McBeth 1912) Bergey et al. 1923 is the type species of the genus Cellulomonas of the actinobacterial family Cellulomonadaceae. Members of the genus Cellulomonas are of special interest for their ability to degrade cellulose and hemicellulose, particularly with regard to the use of biomass as an alternative energy source. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the genus Cellulomonas, and next to the human pathogen Tropheryma whipplei the second complete genome sequence within the actinobacterial family Cellulomonadaceae. The 4,123,179 bp long single replicon genome with its 3,735 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  11. Complete genome sequence of Cellulomonas flavigena type strain (134).

    PubMed

    Abt, Birte; Foster, Brian; Lapidus, Alla; Clum, Alicia; Sun, Hui; Pukall, Rüdiger; Lucas, Susan; Glavina Del Rio, Tijana; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Goodwin, Lynne; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D; Rohde, Manfred; Göker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-07-29

    Cellulomonas flavigena (Kellerman and McBeth 1912) Bergey et al. 1923 is the type species of the genus Cellulomonas of the actinobacterial family Cellulomonadaceae. Members of the genus Cellulomonas are of special interest for their ability to degrade cellulose and hemicellulose, particularly with regard to the use of biomass as an alternative energy source. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the genus Cellulomonas, and next to the human pathogen Tropheryma whipplei the second complete genome sequence within the actinobacterial family Cellulomonadaceae. The 4,123,179 bp long single replicon genome with its 3,735 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  12. Complete genome sequence of Cellulomonas flavigena type strain (134T)

    PubMed Central

    Abt, Birte; Foster, Brian; Lapidus, Alla; Clum, Alicia; Sun, Hui; Pukall, Rüdiger; Lucas, Susan; Glavina Del Rio, Tijana; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Goodwin, Lynne; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Rohde, Manfred; Göker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter

    2010-01-01

    Cellulomonas flavigena (Kellerman and McBeth 1912) Bergey et al. 1923 is the type species of the genus Cellulomonas of the actinobacterial family Cellulomonadaceae. Members of the genus Cellulomonas are of special interest for their ability to degrade cellulose and hemicellulose, particularly with regard to the use of biomass as an alternative energy source. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the genus Cellulomonas, and next to the human pathogen Tropheryma whipplei the second complete genome sequence within the actinobacterial family Cellulomonadaceae. The 4,123,179 bp long single replicon genome with its 3,735 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:21304688

  13. The diversity and biogeography of the communities of Actinobacteria in the forelands of glaciers at a continental scale

    NASA Astrophysics Data System (ADS)

    Zhang, Binglin; Wu, Xiukun; Zhang, Gaosen; Li, Shuyan; Zhang, Wei; Chen, Ximing; Sun, Likun; Zhang, Baogui; Liu, Guangxiu; Chen, Tuo

    2016-05-01

    Glacier forelands, where the initially exposed area is unvegetated with minimal human influence, are an ideal place for research on the distributions and biogeography of microbial communities. Actinobacteria produce many bioactive substances and have important roles in soil development and biogeochemical cycling. However, little is known about the distribution and biogeography of Actinobacteria in glacier forelands. Therefore, we investigated the patterns of diversity and the biogeography of actinobacterial communities of the inhabited forefields of 5 glaciers in China. Of the bacteria, the mean relative abundance of Actinobacteria was 13.1%, and 6 classes were identified in the phylum Actinobacteria. The dominant class was Actinobacteria (57%), which was followed in abundance by Acidimicrobiia (19%) and Thermoleophilia (19%). When combined, the relative abundance of the other three classes, the MB-A2-108, Nitriliruptoria and Rubrobacteria, was only 2.4%. A biogeographic pattern in the forelands of the 5 glaciers in China was not detected for actinobacterial communities. Compared with 7 other actinobacterial communities found in the forelands of glaciers globally, those in the Southern Hemisphere were significantly different from those in the Northern Hemisphere. Moreover, the communities were significantly different on the separate continents of the Northern Hemisphere. The dissimilarity of the actinobacterial communities increased with geographic distance (r = 0.428, p = 0.0003). Because of environmental factors, the effect of geography was clear when the distance exceeded a certain continent-level threshold. With the analysis of indicator species, we found that each genus had a geographic characteristic, which could explain why the communities with greater diversity were more strongly affected by biogeography.

  14. Genome Sequence of “Candidatus Aquiluna” sp. Strain IMCC13023, a Marine Member of the Actinobacteria Isolated from an Arctic Fjord

    PubMed Central

    Kang, Ilnam; Lee, Kiyoung; Yang, Seung-Jo; Choi, Ahyoung; Kang, Dongmin; Lee, Yoo Kyoung

    2012-01-01

    We report the genome sequence of actinobacterial strain IMCC13023, isolated from arctic fjord seawater. Phylogenetic analysis of 16S rRNA gene showed that the strain is related to “Candidatus Aquiluna rubra.” The genome information suggests that strain IMCC13023 is a photoheterotroph carrying actinorhodopsin, with the smallest genome ever reported for a free-living member of the Actinobacteria. PMID:22689238

  15. Biomedical Applications of Enzymes From Marine Actinobacteria.

    PubMed

    Kamala, K; Sivaperumal, P

    2017-01-01

    Marine microbial enzyme technologies have progressed significantly in the last few decades for different applications. Among the various microorganisms, marine actinobacterial enzymes have significant active properties, which could allow them to be biocatalysts with tremendous bioactive metabolites. Moreover, marine actinobacteria have been considered as biofactories, since their enzymes fulfill biomedical and industrial needs. In this chapter, the marine actinobacteria and their enzymes' uses in biological activities and biomedical applications are described.

  16. Actinobacteria Associated with the Marine Sponges Cinachyra sp., Petrosia sp., and Ulosa sp. and Their Culturability

    PubMed Central

    Khan, Shams Tabrez; Takagi, Motoki; Shin-ya, Kazuo

    2012-01-01

    Actinobacteria associated with 3 marine sponges, Cinachyra sp., Petrosia sp., and Ulosa sp., were investigated. Analyses of 16S rRNA gene clone libraries revealed that actinobacterial diversity varied greatly and that Ulosa sp. was most diverse, while Cinachyra sp. was least diverse. Culture-based approaches failed to isolate actinobacteria from Petrosia sp. or Ulosa sp., but strains belonging to 10 different genera and 3 novel species were isolated from Cinachyra sp. PMID:22214828

  17. High-quality draft genome sequence of Kocuria marina SO9-6, an actinobacterium isolated from a copper mine

    PubMed Central

    Castro, Daniel B.A.; Pereira, Letícia Bianca; Silva, Marcus Vinícius M. e; Silva, Bárbara P. da; Palermo, Bruna Rafaella Z.; Carlos, Camila; Belgini, Daiane R.B.; Limache, Elmer Erasmo G.; Lacerda, Gileno V. Jr; Nery, Mariana B.P.; Gomes, Milene B.; Souza, Salatiel S. de; Silva, Thiago M. da; Rodrigues, Viviane D.; Paulino, Luciana C.; Vicentini, Renato; Ferraz, Lúcio F.C.; Ottoboni, Laura M.M.

    2015-01-01

    An actinobacterial strain, designated SO9-6, was isolated from a copper iron sulfide mineral. The organism is Gram-positive, facultatively anaerobic, and coccoid. Chemotaxonomic and phylogenetic properties were consistent with its classification in the genus Kocuria. Here, we report the first draft genome sequence of Kocuria marina SO9-6 under accession JROM00000000 (http://www.ncbi.nlm.nih.gov/nuccore/725823918), which provides insights for heavy metal bioremediation and production of compounds of biotechnological interest. PMID:26484219

  18. High-quality draft genome sequence of Kocuria marina SO9-6, an actinobacterium isolated from a copper mine.

    PubMed

    Castro, Daniel B A; Pereira, Letícia Bianca; Silva, Marcus Vinícius M E; Silva, Bárbara P da; Palermo, Bruna Rafaella Z; Carlos, Camila; Belgini, Daiane R B; Limache, Elmer Erasmo G; Lacerda, Gileno V Jr; Nery, Mariana B P; Gomes, Milene B; Souza, Salatiel S de; Silva, Thiago M da; Rodrigues, Viviane D; Paulino, Luciana C; Vicentini, Renato; Ferraz, Lúcio F C; Ottoboni, Laura M M

    2015-09-01

    An actinobacterial strain, designated SO9-6, was isolated from a copper iron sulfide mineral. The organism is Gram-positive, facultatively anaerobic, and coccoid. Chemotaxonomic and phylogenetic properties were consistent with its classification in the genus Kocuria. Here, we report the first draft genome sequence of Kocuria marina SO9-6 under accession JROM00000000 (http://www.ncbi.nlm.nih.gov/nuccore/725823918), which provides insights for heavy metal bioremediation and production of compounds of biotechnological interest.

  19. Structural and Phylogenetic Analysis of a Conserved Actinobacteria-Specific Protein (ASP1; SCO1997) from Streptomyces Coelicolor

    SciTech Connect

    Gao, B.; Sugiman-Marangos, S; Junop, M; Gupta, R

    2009-01-01

    The Actinobacteria phylum represents one of the largest and most diverse groups of bacteria, encompassing many important and well-characterized organisms including Streptomyces, Bifidobacterium, Corynebacterium and Mycobacterium. Members of this phylum are remarkably diverse in terms of life cycle, morphology, physiology and ecology. Recent comparative genomic analysis of 19 actinobacterial species determined that only 5 genes of unknown function uniquely define this large phylum [1]. The cellular functions of these actinobacteria-specific proteins (ASP) are not known.

  20. Ubiquity, diversity and physiological characteristics of Geodermatophilaceae in Shapotou National Desert Ecological Reserve.

    PubMed

    Sun, Hong-Min; Zhang, Tao; Yu, Li-Yan; Sen, Keya; Zhang, Yu-Qin

    2015-01-01

    The goal of this study was to gain insight into the diversity of culturable actinobacteria in desert soil crusts and to determine the physiological characteristics of the predominant actinobacterial group in these crusts. Culture-dependent method was employed to obtain actinobacterial strains from desert soil samples collected from Shapotou National Desert Ecological Reserve (NDER) located in Tengger Desert, China. A total of 376 actinobacterial strains were isolated and 16S rRNA gene sequences analysis indicated that these isolates belonged to 29 genera within 18 families, among which the members of the family Geodermatophilaceae were predominant. The combination of 16S rRNA gene information and the phenotypic data allowed these newly-isolated Geodermatophilaceae members to be classified into 33 "species clusters," 11 of which represented hitherto unrecognized species. Fermentation broths from 19.7% of the isolated strains showed activity in at least one of the six screens for antibiotic activity. These isolates exhibited bio-diversity in enzymatic characteristics and carbon utilization profiles. The physiological characteristics of the isolates from different types of crusts or bare sand samples were specific to their respective micro-ecological environments. Our study revealed that members of the family Geodermatophilaceae were ubiquitous, abundant, and diverse in Shapotou NDER, and these strains may represent a new major group of potential functional actinobacteria in desert soil.

  1. Involvement of Cell Surface Structures in Size-Independent Grazing Resistance of Freshwater Actinobacteria▿ †

    PubMed Central

    Tarao, Mitsunori; Jezbera, Jan; Hahn, Martin W.

    2009-01-01

    We compared the influences of grazing by the bacterivorous nanoflagellate Poterioochromonas sp. strain DS on ultramicrobacterial Actinobacteria affiliated with the Luna-2 cluster and ultramicrobacterial Betaproteobacteria of the species Polynucleobacter cosmopolitanus. These bacteria were almost identical in size (<0.1 μm3) and shape. Predation on a Polynucleobacter strain resulted in a reduction of >86% relative to the initial bacterial cell numbers within 20 days, while in comparable predation experiments with nine actinobacterial strains, no significant decrease of cell numbers by predation was observed over the period of ≥39 days. The differences in predation mortality between the actinobacterial strains and the Polynucleobacter strain clearly demonstrated size-independent grazing resistance for the investigated Actinobacteria. Importantly, this size-independent grazing resistance is shared by all nine investigated Luna-2 strains and thus represents a group-specific trait. We investigated if an S-layer, previously observed in an ultrastructure study, was responsible for the grazing resistance of these strains. Experiments aiming for removal of the S-layer or modification of cell surface proteins of one of the grazing-resistant strains by treatment with lithium chloride, EDTA, or formaldehyde resulted in 4.2- to 5.2-fold higher grazing rates in comparison to the levels for untreated cells. These results indicate the protective role of a proteinaceous cell surface structure in the size-independent grazing resistance of the actinobacterial Luna-2 strains, which can be regarded as a group-specific trait. PMID:19502450

  2. Phylogenetic diversity of actinobacteria associated with soft coral Alcyonium gracllimum and stony coral Tubastraea coccinea in the East China Sea.

    PubMed

    Yang, Shan; Sun, Wei; Tang, Cen; Jin, Liling; Zhang, Fengli; Li, Zhiyong

    2013-07-01

    Actinobacteria are widely distributed in the marine environment. To date, few studies have been performed to explore the coral-associated Actinobacteria, and little is known about the diversity of coral-associated Actinobacteria. In this study, the actinobacterial diversity associated with one soft coral Alcyonium gracllimum and one stony coral Tubastraea coccinea collected from the East China Sea was investigated using both culture-independent and culture-dependent approaches. A total of 19 actinobacterial genera were detected in these two corals, among which nine genera (Corynebacterium, Dietzia, Gordonia, Kocuria, Microbacterium, Micrococcus, Mycobacterium, Streptomyces, and Candidatus Microthrix) were common, three genera (Cellulomonas, Dermatophilus, and Janibacter) were unique to the soft coral, and seven genera (Brevibacterium, Dermacoccus, Leucobacter, Micromonospora, Nocardioides, Rhodococcus, and Serinicoccus) were unique to the stony coral. This finding suggested that highly diverse Actinobacteria were associated with different types of corals. In particular, five actinobacterial genera (Cellulomonas, Dermacoccus, Gordonia, Serinicoccus, and Candidatus Microthrix) were recovered from corals for the first time, extending the known diversity of coral-associated Actinobacteria. This study shows that soft and stony corals host diverse Actinobacteria and can serve as a new source of marine actinomycetes.

  3. Potential of Cometabolic Transformation of Polysaccharides and Lignin in Lignocellulose by Soil Actinobacteria

    PubMed Central

    Větrovský, Tomáš; Steffen, Kari Timo; Baldrian, Petr

    2014-01-01

    While it is known that several Actinobacteria produce enzymes that decompose polysaccharides or phenolic compounds in dead plant biomass, the occurrence of these traits in the environment remains largely unclear. The aim of this work was to screen isolated actinobacterial strains to explore their ability to produce extracellular enzymes that participate in the degradation of polysaccharides and their ability to cometabolically transform phenolic compounds of various complexities. Actinobacterial strains were isolated from meadow and forest soils and screened for their ability to grow on lignocellulose. The potential to transform 14C-labelled phenolic substrates (dehydrogenation polymer (DHP), lignin and catechol) and to produce a range of extracellular, hydrolytic enzymes was investigated in three strains of Streptomyces spp. that possessed high lignocellulose degrading activity. Isolated strains showed high variation in their ability to produce cellulose- and hemicellulose-degrading enzymes and were able to mineralise up to 1.1% and to solubilise up to 4% of poplar lignin and to mineralise up to 11.4% and to solubilise up to 64% of catechol, while only minimal mineralisation of DHP was observed. The results confirm the potential importance of Actinobacteria in lignocellulose degradation, although it is likely that the decomposition of biopolymers is limited to strains that represent only a minor portion of the entire community, while the range of simple, carbon-containing compounds that serve as sources for actinobacterial growth is relatively wide. PMID:24551229

  4. Environmental Sensing in Actinobacteria: a Comprehensive Survey on the Signaling Capacity of This Phylum

    PubMed Central

    Huang, Xiaoluo; Pinto, Daniela; Fritz, Georg

    2015-01-01

    ABSTRACT Signal transduction is an essential process that allows bacteria to sense their complex and ever-changing environment and adapt accordingly. Three distinct major types of signal-transducing proteins (STPs) can be distinguished: one-component systems (1CSs), two-component systems (2CSs), and extracytoplasmic-function σ factors (ECFs). Since Actinobacteria are particularly rich in STPs, we comprehensively investigated the abundance and diversity of STPs encoded in 119 actinobacterial genomes, based on the data stored in the Microbial Signal Transduction (MiST) database. Overall, we observed an approximately linear correlation between the genome size and the total number of encoded STPs. About half of all membrane-anchored 1CSs are protein kinases. For both 1CSs and 2CSs, a detailed analysis of the domain architectures identified novel proteins that are found only in actinobacterial genomes. Many actinobacterial genomes are particularly enriched for ECFs. As a result of this study, almost 500 previously unclassified ECFs could be classified into 18 new ECF groups. This comprehensive survey demonstrates that actinobacterial genomes encode previously unknown STPs, which may represent new mechanisms of signal transduction and regulation. This information not only expands our knowledge of the diversity of bacterial signal transduction but also provides clear and testable hypotheses about their mechanisms, which can serve as starting points for experimental studies. IMPORTANCE In the wake of the genomic era, with its enormous increase in the amount of available sequence information, the challenge has now shifted toward making sense and use of this treasure chest. Such analyses are a prerequisite to provide meaningful information that can help guide subsequent experimental efforts, such as mechanistic studies on novel signaling strategies. This work provides a comprehensive analysis of signal transduction proteins from 119 actinobacterial genomes. We identify

  5. Metagenomic Classification and Characterization Marine Actinobacteria from the Gulf of Maine without Representative Genomes

    NASA Astrophysics Data System (ADS)

    Sachdeva, R.; Heidelberg, J.

    2012-12-01

    Actinobacteria represent one of the largest and most diverse bacterial phyla and unlike most marine prokaryotes are gram-positive. This phylum encompasses a broad range of physiologies, morphologies, and metabolic properties with a broad array of lifestyles. The marine actinobacterial assemblage is dominated by the orders Actinomycetales and Acidimicrobiales (also known as the marine Actinobacteria clade). The Acidimicrobiales bacteria typically outnumber the Actinomycetales bacteria and are mostly represented by the OCS155 group. Although bacteria of the order Acidimicrobiales make up ~7.6% of the 16S matches from the Global Ocean Survey shotgun metagenomic libraries; very little is known about their potential function and role in biogeochemical cycling. Samples were collected from surface seawater samples in the Gulf of Maine (GOM) from the summer and winter of 2006. Sanger sequences were generated from the 0.1-0.8 μm fractions using paired-end medium insert shotgun libraries. The resulting 2.2 Gb were assembled using the Celera Assembler package into 280 Mb of non-redundant scaffolds. Putative actinobacterial assemblies were identified using (1) ribosomal RNA genes (16S and 23S), (2) phylogenetically informative non-ribosomal core genes thought to be resistant to horizontal gene transfer (e.g. RecA and RpoB) and (3) compositional binning using oligonucleotide frequency pattern based hierarchical clustering. Binning resulted in 3.6 Mb (4.2X coverage) of actinobacterial scaffolds that were comprised of 15.1 Mb of unassembled reads. Putative actinobacterial assemblies included both summer and winter reads demonstrating that the Actinobacteria are abundant year round. Classification reveals that all of the sampled Actinobacteria are from the orders Acidimicrobiales and Actinomycetales and are similar to those found in the global ocean. The GOM Actinobacteria show a broad range of G+C % content (32-66%) indicating a high level of genomic diversity. Those assemblies

  6. Reconstructing labroid evolution with single-copy nuclear DNA.

    PubMed Central

    Streelman, J T; Karl, S A

    1997-01-01

    Fifteen per cent of all living fishes are united in a single suborder (Labroidei) and display a dazzling array of behavioural and ecological traits. The labroids are considered monophyletic and members share a pharyngeal jaw apparatus (PJA) modified for crushing and processing prey. Outside of the explicitly functional PJA, there is no corroborative evidence for a monophyletic Labroidei. Here, we report the first molecular phylogenetic analysis of the suborder. Contrary to morphology-based phylogenies, our single-copy nuclear DNA data do not support labroid families as a natural group. Our data indicate that pharyngognathy has evolved independently among labroid families and that characters of the PJA are not reliable markers of perciform evolution. This work 'crushes' conventional views of fish phylogeny and should engender novel concepts of piscine life history evolution. PMID:9263469

  7. Chromosomes of Lepidochitona caprearum (Scacchi, 1836) (Polyplacophora, Acanthochitonina, Tonicellidae) provide insights into Acanthochitonina karyological evolution.

    PubMed

    Petraccioli, Agnese; Maio, Nicola; Odierna, Gaetano

    2012-01-01

    We describe the karyotype, location of nucleolus-organizing regions (NORs) and heterochromatin composition and distribution in Lepidochitona caprearum (Scacchi, 1836). The examined specimens had 2n=24 chromosomes; the elements of pairs 1-4 were metacentric, subtelocentric those of the fifth pair, telocentric the elements of other pairs. NOR-FISH, Ag-NOR- and CMA3 banding showed NORs localized on pericentromeric regions of a medium small sized, telocentric chromosome pair. After C-banding or digestions with restriction enzyme NOR associate heterochromatin only was cytologically evident, resulting CMA3 positive. The comparison with chromosome data of other chitons, other than to evidence a karyotypic similarity of Lepidochitona caprearum to species of suborder Acanthochitonina, allows us to infer that chromosome evolution in the suborder mainly occurred via reduction of the number of the chromosomes by centric fusions, which took place repeatedly and independently in the different lineages of Acanthochitonina.

  8. Comparative and functional morphology of wing coupling structures in Trichoptera: Annulipalpia.

    PubMed

    Stocks, Ian C

    2010-02-01

    Several orders of morphologically four-winged insects have evolved mechanisms that enforce a union between the mesothoracic and metathoracic wings (forewings and hindwings) during the wing beat cycle. Such mechanisms result in a morphologically tetrapterous insect flying as if it were functionally dipterous, and these mechanisms have been described for several insect orders. The caddisfly suborders Annulipalpia and Integripalpia (Trichoptera) each have evolved a wing coupling apparatus, with at least three systems having evolved within the suborder Annulipalpia. The comparative and inferred functional morphology of the putative wing coupling mechanisms is described for the annulipalpian families Hydropsychidae (subfamilies Macronematinae and Hydropsychinae), Polycentropodidae and Ecnomidae, and a novel form-functional complex putatively involved with at-rest forewing-forewing coupling is described for Hydropsychidae: Smicrideinae. It is proposed that the morphology of the wing coupling apparatuses of Hydropsychinae and Macronematinae are apomorphies for those clades.

  9. A Sarcocystid misidentified as Hepatozoon didelphydis: molecular data from a parasitic infection in the blood of the Southern mouse opossum (Thylamys elegans) from Chile.

    PubMed

    Merino, Santiago; Vásquez, Rodrigo A; Martínez, Javier; Celis-Diez, Juan L; Martínez-de la Puente, Josué; Marín-Vial, Paula; Sánchez-Monsalvez, Inocencia; Peirce, Michael A

    2008-01-01

    The blood of 21 adult South American mouse opossums (Thylamys elegans) captured from April through August of 2005 in central Chile was examined for parasites. Light microscopic analysis of blood smears initially suggested that a highly pleomorphic Hepatozoon species typical of American opossums was infecting erythrocytes. Unexpectedly, amplification by PCR and sequencing of a DNA fragment of the small subunit rDNA combined with phylogenetic analyses indicated that the parasite is not a member of the suborder Adeleorina, which includes the Haemogregarina and Hepatozoon species, but that it is a clearly distinct member of the suborder Eimeriorina, which includes the cyst-forming family Sarcocystidae. Therefore, a reclassification of this unusual intraerythrocytic apicomplexan will require additional life cycle, microscopic, and molecular analyses.

  10. Widespread Losses of Vomeronasal Signal Transduction in Bats

    PubMed Central

    Zhao, Huabin; Xu, Dong; Zhang, Shuyi; Zhang, Jianzhi

    2011-01-01

    The vertebrate vomeronasal system (VNS) detects intraspecific pheromones and environmental odorants. We sequenced segments of the gene encoding Trpc2, an ion channel crucial for vomeronasal signal transduction, in 11 species that represent all main basal lineages of Yinpterochiroptera, one of the two suborders of the order Chiroptera (bats). Our sequences show that Trpc2 is a pseudogene in each of the 11 bats, suggesting that all yinpterochiropterans lack vomeronasal sensitivity. The Trpc2 sequences from four species of Yangochiroptera, the other suborder of bats, suggest vomeronasal insensitivity in some but not all yangochiropterans. These results, together with the available morphological data from the bat VNS, strongly suggest multiple and widespread losses of vomeronasal signal transduction and sensitivity in bats. Future scrutiny of the specific functions of the VNS in the few bats that still retain the VNS may help explain why it is dispensable in most bats. PMID:20693241

  11. The complete mitochondrial genome of Dixella aestivalis (Diptera: Nematocera: Dixidae).

    PubMed

    Briscoe, Andrew G; Sivell, Duncan; Harbach, Ralph E

    2017-01-01

    Dixidae, meniscus midges, belong to the suborder Nematocera of the order Diptera. The family includes 197 known species classified in nine genera. The complete mitochondrial genome of the Dixella aestivalis (Meigen) from the United Kingdom is reported here, along with its annotation and comparison with the genome of an unidentified species of Dixella from China. The circular genome consists of 16 465 bp and has a gene content consisting of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a non-coding, A + T-rich, control region. The mitochondrial genome of D. aestivalis can be used to identify genetic markers for species identification, and will be valuable for resolving phylogenetic relationships within the genus, family Dixidae and suborder Nematocera.

  12. Chromosomes of Lepidochitona caprearum (Scacchi, 1836) (Polyplacophora, Acanthochitonina, Tonicellidae) provide insights into Acanthochitonina karyological evolution

    PubMed Central

    Petraccioli, Agnese; Maio, Nicola; Odierna, Gaetano

    2012-01-01

    Abstract We describe the karyotype, location of nucleolus-organizing regions (NORs) and heterochromatin composition and distribution in Lepidochitona caprearum (Scacchi, 1836). The examined specimens had 2n=24 chromosomes; the elements of pairs 1–4 were metacentric, subtelocentric those of the fifth pair, telocentric the elements of other pairs. NOR-FISH, Ag-NOR- and CMA3 banding showed NORs localized on pericentromeric regions of a medium small sized, telocentric chromosome pair. After C-banding or digestions with restriction enzyme NOR associate heterochromatin only was cytologically evident, resulting CMA3 positive. The comparison with chromosome data of other chitons, other than to evidence a karyotypic similarity of Lepidochitona caprearum to species of suborder Acanthochitonina, allows us to infer that chromosome evolution in the suborder mainly occurred via reduction of the number of the chromosomes by centric fusions, which took place repeatedly and independently in the different lineages of Acanthochitonina. PMID:24260680

  13. Chewing lice (Phthiraptera: Amblycera, Ischnocera) from Red Sea gulls with new host-parasite records.

    PubMed

    Al-Ahmed, Azzam; Shobrak, Mohammed; Nasser, Mohamed G E-D

    2014-04-23

    Knowledge about chewing lice from marine birds of the Red Sea is minimal. Five species of gulls were examined for chewing lice in three different localities of the Saudi Arabian Red Sea coast. Two gull species were examined for lice for the first time (Larus armenicus Buturlin, 1934 and Larus michahellis Naumann, 1840) and their lice represent new host-louse associations. Four species and two subspecies of lice were identified from 159 specimens collected. Actornithophilus piceus lari (Packard, 1870) and Austromenopon transversum (Denny, 1842) (suborder: Amblycera), and Quadraceps punctatus (Burmeister, 1838) and Saemundssonia lari (O. Fabricius, 1780) (suborder: Ischnocera) were recorded for the first time from Saudi Arabia and Red Sea birds. Taxonomic and ecological notes, type hosts, data on specimens examined, collecting localities, an identification key, and photographs of each species and subspecies are given. 

  14. Extant cheilostomatous bryozoans of the Middle Miocene from the north Western Desert, Egypt

    NASA Astrophysics Data System (ADS)

    Ziko, Abdelmohsen; Eweda, Shehta; El-Khawaga, Samar

    2016-12-01

    Twenty-nine extant Bryozoan species, belonging to the order Cheilostomata are described. They are from the Middle Miocene Marmarica Formation of the northern Western Desert in Egypt. The described bryozoans are collected from Matruh and Siwa areas. Fourteen species belong to the suborder Anasca, and the other fifteen species belong to the suborder Ascophora. The identified bryozoan species exhibit many zoarial growth forms. The encrusting forms are membraniporiform and celleporiform, while the erect forms are adeoniforms, eschariforms, vinculariiforms, reteporiform, and cellariiforms. They extend in the geologic record from the Eocene to the Recent, distributed mainly in the Tethyan realm, and recorded also from North America. The extant species are mainly of Mediterranean affinity, some are of wider distribution in the Atlantic and Pacific oceans, and are rarely cosmopolitan.

  15. Plant mites of the Dominican Republic, with a description of a new species of Petrobia (Tetranychina) Wainstein, 1960 (Acari, Prostigmata, Tetranychidae) and a key to the species of this subgenus.

    PubMed

    Martínez, Leocadia Sánchez; Flechtmann, Carlos H W; De Moraes, Gilberto J

    2014-08-05

    Fourteen mite species of plant-associated mites of the suborder Prostigmata are reported from the Dominican Republic. Four of these refer to new findings for the country, including Petrobia (Tetranychina) hispaniola n. sp. Sánchez & Flechtmann, described from specimens collected from leaves of Citrus sp. (Rutaceae) and Rosa sp. (Rosaceae). A key for the separation of the world species of Petrobia (Tetranychina) is presented. 

  16. Valve microstructure and phylomineralogy of New Zealand chitons.

    PubMed

    Peebles, B A; Smith, A M; Spencer, H G

    2017-03-01

    The microstructure and mineralogy of chiton valves has been largely ignored in the literature and only described in 29 species to date. Eight species: Acanthochitona zelandica, Notoplax violacea (Family Acanthochitonidae, Suborder Acanthochitonina, Order Chitonida), Chiton glaucus, Onithochiton neglectus, Sypharochiton spelliserpentis, Sypharochiton sinclairi (Family Chitonidae, Suborder, Chitonina, Order Chitonida), Ischnochiton maorianus (Family Ischnochitonidae, Suborder Chitonina, Order Chitonida), and Leptochiton inquinatus (Family Leptochitonidae, Suborder Lepidopleurina, Order Lepidopleurida) were collected from the Otago Peninsula, South Island, New Zealand. The valves of these chitons were analysed with X-ray diffractometry, Raman spectrometry, and Scanning Electron Micrography (SEM) to determine their mineralogy and microstructure. Both the XRD and Raman data show that the valves consisted solely of aragonite. The observed microstructures of the valves were complex, typically composed of four to seven sublayers, and varied among species. The dorsal layer, the tegmentum, of each species was granular and the ventral layer, the articulamentum, was predominately composed of a spherulitic sublayer, a crossed lamellar sublayer, and an acicular sublayer. The chitonids Sypharochiton pelliserpentis and S. sinclairi had the most complex microstructure layering with three crossed lamellar, two spherulitic sublayers, and a ventral acicular sublayer while the acanthochitonids Acanthochitona zelandica and Notoplax violacea as well as the ischnochitonid Ischnochiton maorianus had the simplest structure with one spherulitic, one crossed lamellar sublayer, and a ventral acicular sublayer. Terminal valves were less complex than intermediate valves and tended to be dominated by the crossed lamellar structure. The leptochitonid Leptochiton inquinatus generated a unique crossed lamellar sublayer different from the other analysed chitonids. Acanthochitona zelandica is the only

  17. Site Evaluation Studies of the Massachusetts Bay Disposal Site for Ocean Disposal of Dredged Material

    DTIC Science & Technology

    1988-07-05

    Suborder Odontoceti (Toothed Whales) Family Delphinidae Family Monodontidae Beluga (Delphinapterus leucas) Family Physeteridae Pygmy Sperm Whale (Kogia...Whales) Family Delphinidae Family Monodontidae Beluga Delphinapterus leucas Family Physeteridae Pygmy Sperm Whale Kogia breviceps Family Ziphiidae...smaller cetacea in Greenland. J. Fish. Res. Bd. Canada 32:1079-1082. Kapel, F.O. 1977. Catch of beluga , narwhals and harbor porpoises in Greenland, 1954-75

  18. First Record of Anisoptera (Insecta: Odonata) from mid-Cretaceous Burmese Amber.

    PubMed

    Schädel, Mario; Bechly, Günter

    2016-04-18

    The fossil dragonfly Burmalindenia imperfecta gen. et sp. nov. is described from mid-Cretaceous Burmese amber as the first record of the odonate suborder Anisoptera for this locality and one of the few records from amber in general. The inclusion comprises two fragments of the two hind wings of a dragonfly. The fossil can be attributed to a new genus and species of the family Gomphidae, presumably in the subfamily Lindeniinae, and features a strange teratological phenomenon in its wing venation.

  19. White piedra and pediculosis capitis in the same patient.

    PubMed

    Marques, Silvio Alencar; Richini-Pereira, Virgínia Bodelão; Camargo, Rosângela Maria Pires de

    2012-01-01

    White piedra is a superficial mycosis caused by the genus Trichosporon. It is characterized by nodules on the hair shaft. Pediculosis capitis is caused by Pediculus humanus var. capitis of the suborder Anoplura. Whereas pediculosis is a common infestation, clinical reports of white piedra are rare. Molecular biology procedures identified T. inkin as the agent of white piedra in this case report. The authors present associations between the two diseases in the same patient in order to highlight their clinical differences.

  20. Evolutionary transitions in symbioses: dramatic reductions in bathymetric and geographic ranges of Zoanthidea coincide with loss of symbioses with invertebrates.

    PubMed

    Swain, Timothy D

    2010-06-01

    Two fundamental symbiosis-based trophic types are recognized among Zoanthidea (Cnidaria, Anthozoa): fixed carbon is either obtained directly from zooxanthellae photosymbionts or from environmental sources through feeding with the assistance of host-invertebrate behaviour and structure. Each trophic type is characteristic of the suborders of Zoanthidea and is associated with substantial distributional asymmetries: suborder Macrocnemina are symbionts of invertebrates and have global geographic and bathymetric distributions and suborder Brachycnemina are hosts of endosymbiotic zooxanthellae and are restricted to tropical photic zones. While exposure to solar radiation could explain the bathymetric asymmetry it does not explain the geographic asymmetry, nor is it clear why evolutionary transitions to the zooxanthellae-free state have apparently occurred within Macrocnemina but not within Brachycnemina. To better understand the transitions between symbiosis-based trophic types of Zoanthidea, a concatenated data set of nuclear and mitochondrial nucleotide sequences were used to test hypotheses of monophyly for groups defined by morphology and symbiosis, and to reconstruct the evolutionary transitions of morphological and symbiotic characters. The results indicate that the morphological characters that define Macrocnemina are plesiomorphic and the characters that define its subordinate taxa are homoplasious. Symbioses with invertebrates have ancient and recent transitions with a general pattern of stability in host associations through evolutionary time. The reduction in distribution of Zoanthidea is independent of the evolution of zooxanthellae symbiosis and consistent with hypotheses of the benefits of invertebrate symbioses, indicating that the ability to persist in most habitats may have been lost with the termination of symbioses with invertebrates.

  1. The early evolutionary history of belemnites: new data from Japan.

    PubMed

    Iba, Yasuhiro; Sano, Shin-ichi; Mutterlose, Jörg

    2014-01-01

    Belemnites (Order Belemnitida), a very successful group of Mesozoic coleoid cephalopods, dominated the world's oceans throughout the Jurassic and Cretaceous. According to the current view, the phylogenetically earliest belemnites are known from the lowermost Jurassic (Hettangian, 201-199 Ma) of northern Europe. They are of low diversity and have small sized rostra without clear grooves. Their distribution is restricted to this area until the Pliensbachian (191-183 Ma). Here we describe two new belemnite taxa of the Suborder Belemnitina from the Sinemurian (199-191 Ma) of Japan: Nipponoteuthis katana gen et sp. nov., which represents the new family Nipponoteuthidae, and Eocylindroteuthis (?) yokoyamai sp. nov. This is the first reliable report of Sinemurian belemnites outside of Europe and the earliest record of typical forms of Belemnitina in the world. The Sinemurian belemnites from Japan have small to large rostra with one deep and long apical groove. Morphologically these forms are completely different from coeval European genera of Hettangian-Sinemurian age. These new findings suggest that three groups of Belemnitina existed in the Hettangian-Sinemurian: 1) European small forms, 2) Japanese very large forms, and 3) the typical forms with a distinctive apical groove, reported here. The Suborder Belemnitina therefore did not necessarily originate in the Hettangian of northern Europe. The new material from Japan documents that the suborder Belemnitina had a much higher diversity in the early Jurassic than previously thought, and it also shows strong endemisms from the Sinemurian onwards.

  2. Prevention of Gordonia and Nocardia Stabilized Foam Formation by Using Bacteriophage GTE7▿†

    PubMed Central

    Petrovski, Steve; Seviour, Robert J.; Tillett, Daniel

    2011-01-01

    Most activated sludge treatment plants suffer from the presence of foams on the surfaces of their aeration reactors. These are often stabilized by hydrophobic mycolic acid-synthesizing actinobacterial species. A polyvalent Siphoviridae phage, GTE7, which lysed several Gordonia and Nocardia species, is described here. Its genome has a modular structure similar to that described for Rhodococcus phage ReqiDocB7. In laboratory-scale experiments, we showed that GTE7 prevents stabilization of foams by these Gordonia and Nocardia species. PMID:21926218

  3. Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07T)

    SciTech Connect

    Foster, Brian; Pukall, Rudiger; Abt, Birte; Nolan, Matt; Glavina Del Rio, Tijana; Chen, Feng; Lucas, Susan; Tice, Hope; Pitluck, Sam; Cheng, Jan-Fang; Chertkov, Olga; Brettin, Thomas S; Han, Cliff; Detter, J C; Bruce, David; Goodwin, Lynne A.; Ivanova, N; Mavromatis, K; Pati, Amrita; Mikhailova, Natalia; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Chain, Patrick S. G.; Rohde, Manfred; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lapidus, Alla L.

    2010-01-01

    Xylanimonas cellulosilytica Rivas et al. 2003 is the type species of the genus Xylanimonas of the actinobacterial family Promicromonosporaceae. The species X. cellulosilytica is of interest because of its ability to hydrolyze cellulose and xylan. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the large family Promicromonosporaceae, and the 3,831,380 bp long genome (one chromosome plus an 88,604 bp long plasmid) with its 3485 protein-coding and 61 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  4. Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICPT)

    SciTech Connect

    Clum, Alicia; Nolan, Matt; Lang, Elke; Glavina Del Rio, Tijana; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavrommatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Goker, Markus; Spring, Stefan; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jefferies, Cynthia C.; Chain, Patrick; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Lapidus, Alla

    2009-05-20

    Acidimicrobium ferrooxidans (Clark and Norris 1996) is the sole and type species of the genus, which until recently was the only genus within the actinobacterial family Acidimicrobiaceae and in the order Acidomicrobiales. Rapid oxidation of iron pyrite during autotrophic growth in the absence of an enhanced CO2 concentration is characteristic for A. ferrooxidans. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the order Acidomicrobiales, and the 2,158,157 bp long single replicon genome with its 2038 protein coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  5. Streptomyces fractus sp. nov., a novel streptomycete isolated from the gut of a South African termite.

    PubMed

    Rohland, Jeffrey; Meyers, Paul R

    2015-05-01

    An actinobacterial strain, MV32(T), was isolated from the paunch region of the hindgut of a South African termite, Amitermes hastatus, as part of an investigation of the actinobacterial population residing within this higher order termite species. Strain MV32(T) was chosen for further study from amongst the many potentially novel actinomycete isolates because of its strong antibacterial activity against Mycobacterium aurum A+. 16S rRNA gene phylogenetic analyses clearly placed strain MV32(T) within the genus Streptomyces, with 99.3% sequence similarity to its closest relative, Streptomyces endophyticus YIM 65594(T). Despite this high sequence similarity, DNA-DNA hybridisation analysis showed a DNA relatedness value of 62 ± 2%, to S. endophyticus DSM 41984(T) (indicating that strain MV32(T) belongs to a different genomic species), as well as values of 14.4 ± 0.8 and 10.4 ± 2.9%, respectively, to its next closest relatives, Streptomyces kunmingensis NRRL B-16240(T) and Streptomyces cinnabarinus NRRL B-12382(T). Based on these results and supported by both chemotaxonomic data and a number of phenotypic differences, strain MV32(T) is proposed to represent a new species within the genus Streptomyces, with the name Streptomyces fractus (= DSM 42163(T) = NRRL B-59159(T)).

  6. Vitamin supplementation by gut symbionts ensures metabolic homeostasis in an insect host.

    PubMed

    Salem, Hassan; Bauer, Eugen; Strauss, Anja S; Vogel, Heiko; Marz, Manja; Kaltenpoth, Martin

    2014-12-07

    Despite the demonstrated functional importance of gut microbes, our understanding of how animals regulate their metabolism in response to nutritionally beneficial symbionts remains limited. Here, we elucidate the functional importance of the African cotton stainer's (Dysdercus fasciatus) association with two actinobacterial gut symbionts and subsequently examine the insect's transcriptional response following symbiont elimination. In line with bioassays demonstrating the symbionts' contribution towards host fitness through the supplementation of B vitamins, comparative transcriptomic analyses of genes involved in import and processing of B vitamins revealed an upregulation of gene expression in aposymbiotic (symbiont-free) compared with symbiotic individuals; an expression pattern that is indicative of B vitamin deficiency in animals. Normal expression levels of these genes, however, can be restored by either artificial supplementation of B vitamins into the insect's diet or reinfection with the actinobacterial symbionts. Furthermore, the functional characterization of the differentially expressed thiamine transporter 2 through heterologous expression in Xenopus laevis oocytes confirms its role in cellular uptake of vitamin B1. These findings demonstrate that despite an extracellular localization, beneficial gut microbes can be integral to the host's metabolic homeostasis, reminiscent of bacteriome-localized intracellular mutualists.

  7. Linking Microbial Community and Catabolic Gene Structures during the Adaptation of Three Contaminated Soils under Continuous Long-Term Pollutant Stress

    PubMed Central

    Lima-Morales, Daiana; Jáuregui, Ruy; Camarinha-Silva, Amelia; Geffers, Robert; Vilchez-Vargas, Ramiro

    2016-01-01

    Three types of contaminated soil from three geographically different areas were subjected to a constant supply of benzene or benzene/toluene/ethylbenzene/xylenes (BTEX) for a period of 3 months. Different from the soil from Brazil (BRA) and Switzerland (SUI), the Czech Republic (CZE) soil which was previously subjected to intensive in situ bioremediation displayed only negligible changes in community structure. BRA and SUI soil samples showed a clear succession of phylotypes. A rapid response to benzene stress was observed, whereas the response to BTEX pollution was significantly slower. After extended incubation, actinobacterial phylotypes increased in relative abundance, indicating their superior fitness to pollution stress. Commonalities but also differences in the phylotypes were observed. Catabolic gene surveys confirmed the enrichment of actinobacteria by identifying the increase of actinobacterial genes involved in the degradation of pollutants. Proteobacterial phylotypes increased in relative abundance in SUI microcosms after short-term stress with benzene, and catabolic gene surveys indicated enriched metabolic routes. Interestingly, CZE soil, despite staying constant in community structure, showed a change in the catabolic gene structure. This indicates that a highly adapted community, which had to adjust its gene pool to meet novel challenges, has been enriched. PMID:26850298

  8. Littoral lichens as a novel source of potentially bioactive Actinobacteria.

    PubMed

    Parrot, Delphine; Antony-Babu, Sanjay; Intertaglia, Laurent; Grube, Martin; Tomasi, Sophie; Suzuki, Marcelino T

    2015-10-30

    Cultivable Actinobacteria are the largest source of microbially derived bioactive molecules. The high demand for novel antibiotics highlights the need for exploring novel sources of these bacteria. Microbial symbioses with sessile macro-organisms, known to contain bioactive compounds likely of bacterial origin, represent an interesting and underexplored source of Actinobacteria. We studied the diversity and potential for bioactive-metabolite production of Actinobacteria associated with two marine lichens (Lichina confinis and L. pygmaea; from intertidal and subtidal zones) and one littoral lichen (Roccella fuciformis; from supratidal zone) from the Brittany coast (France), as well as the terrestrial lichen Collema auriforme (from a riparian zone, Austria). A total of 247 bacterial strains were isolated using two selective media. Isolates were identified and clustered into 101 OTUs (98% identity) including 51 actinobacterial OTUs. The actinobacterial families observed were: Brevibacteriaceae, Cellulomonadaceae, Gordoniaceae, Micrococcaceae, Mycobacteriaceae, Nocardioidaceae, Promicromonosporaceae, Pseudonocardiaceae, Sanguibacteraceae and Streptomycetaceae. Interestingly, the diversity was most influenced by the selective media rather than lichen species or the level of lichen thallus association. The potential for bioactive-metabolite biosynthesis of the isolates was confirmed by screening genes coding for polyketide synthases types I and II. These results show that littoral lichens are a source of diverse potentially bioactive Actinobacteria.

  9. Marine Actinobacteria from the Gulf of California: diversity, abundance and secondary metabolite biosynthetic potential.

    PubMed

    Becerril-Espinosa, Amayaly; Freel, Kelle C; Jensen, Paul R; Soria-Mercado, Irma E

    2013-04-01

    The Gulf of California is a coastal marine ecosystem characterized as having abundant biological resources and a high level of endemism. In this work we report the isolation and characterization of Actinobacteria from different sites in the western Gulf of California. We collected 126 sediment samples and isolated on average 3.1-38.3 Actinobacterial strains from each sample. Phylogenetic analysis of 136 strains identified them as members of the genera Actinomadura, Micromonospora, Nocardiopsis, Nonomuraea, Saccharomonospora, Salinispora, Streptomyces and Verrucosispora. These strains were grouped into 26-56 operational taxonomic units (OTUs) based on 16S rRNA gene sequence identities of 98-100 %. At 98 % sequence identity, three OTUs appear to represent new taxa while nine (35 %) have only been reported from marine environments. Sixty-three strains required seawater for growth. These fell into two OTUs at the 98 % identity level and include one that failed to produce aerial hyphae and was only distantly related (≤95.5 % 16S identity) to any previously cultured Streptomyces sp. Phylogenetic analyses of ketosynthase domains associated with polyketide synthase genes revealed sequences that ranged from 55 to 99 % nucleotide identity to experimentally characterized biosynthetic pathways suggesting that some may be associated with the production of new secondary metabolites. These results indicate that marine sediments from the Gulf of California harbor diverse Actinobacterial taxa with the potential to produce new secondary metabolites.

  10. Actinobacteria possessing antimicrobial and antioxidant activities isolated from the pollen of scots pine (Pinus sylvestris) grown on the Baikal shore.

    PubMed

    Axenov-Gribanov, Denis V; Voytsekhovskaya, Irina V; Rebets, Yuriy V; Tokovenko, Bogdan T; Penzina, Tatyana A; Gornostay, Tatyana G; Adelshin, Renat V; Protasov, Eugenii S; Luzhetskyy, Andriy N; Timofeyev, Maxim A

    2016-10-01

    Isolated ecosystems existing under specific environmental conditions have been shown to be promising sources of new strains of actinobacteria. The taiga forest of Baikal Siberia has not been well studied, and its actinobacterial population remains uncharacterized. The proximity between the huge water mass of Lake Baikal and high mountain ranges influences the structure and diversity of the plant world in Siberia. Here, we report the isolation of eighteen actinobacterial strains from male cones of Scots pine trees (Pinus sylvestris) growing on the shore of the ancient Lake Baikal in Siberia. In addition to more common representative strains of Streptomyces, several species belonging to the genera Rhodococcus, Amycolatopsis, and Micromonospora were isolated. All isolated strains exhibited antibacterial and antifungal activities. We identified several strains that inhibited the growth of the pathogen Candida albicans but did not hinder the growth of Saccharomyces cerevisiae. Several isolates were active against Gram-positive and Gram-negative bacteria. The high proportion of biologically active strains producing antibacterial and specific antifungal compounds may reflect their role in protecting pollen against phytopathogens.

  11. RubisCO-based CO2 fixation and C1 metabolism in the actinobacterium Pseudonocardia dioxanivorans CB1190.

    PubMed

    Grostern, Ariel; Alvarez-Cohen, Lisa

    2013-11-01

    Pseudonocardia is an actinobacterial genus of interest due to its potential biotechnological, medical and environmental remediation applications, as well as for the ecologically relevant symbiotic relationships it forms with attine ants. Some Pseudonocardia spp. can grow autotrophically, but the genetic basis of this capability has not previously been reported. In this study, we examined autotrophy in Pseudonocardia dioxanivorans CB1190, which can grow using H2 and CO2, as well as heterotrophically. Genomic and transcriptomic analysis of CB1190 cells grown with H2/bicarbonate implicated the Calvin-Benson-Bassham (CBB) cycle in growth-supporting CO2 fixation, as well as a [NiFe] hydrogenase-encoding gene cluster in H2 oxidation. The CBB cycle genes are evolutionarily most related to actinobacterial homologues, although synteny has not been maintained. Ribulose-1,5-bisphosphate carboxylase activity was confirmed in H2/bicarbonate-grown CB1190 cells and was detected in cells grown with the C1 compounds formate, methanol and carbon monoxide. We also demonstrated the upregulation of CBB cycle genes upon exposure of CB1190 to these C1 substrates, and identified genes putatively involved in generating CO2 from the C1 substrates by using RT-qPCR. Finally, the potential for autotrophic growth of other Pseudonocardia spp. was explored, and the ecological implications of autotrophy in attine ant- and plant root-associated Pseudonocardia discussed.

  12. How to assemble a beneficial microbiome in three easy steps

    PubMed Central

    Scheuring, István; Yu, Douglas W

    2012-01-01

    There is great interest in explaining how beneficial microbiomes are assembled. Antibiotic-producing microbiomes are arguably the most abundant class of beneficial microbiome in nature, having been found on corals, arthropods, molluscs, vertebrates and plant rhizospheres. An exemplar is the attine ants, which cultivate a fungus for food and host a cuticular microbiome that releases antibiotics to defend the fungus from parasites. One explanation posits long-term vertical transmission of P seudonocardia bacteria, which (somehow) evolve new compounds in arms-race fashion against parasites. Alternatively, attines (somehow) selectively recruit multiple, non-coevolved actinobacterial genera from the soil, enabling a ‘multi-drug’ strategy against parasites. We reconcile the models by showing that when hosts fuel interference competition by providing abundant resources, the interference competition favours the recruitment of antibiotic-producing (and -resistant) bacteria. This partner-choice mechanism is more effective when at least one actinobacterial symbiont is vertically transmitted or has a high immigration rate, as in disease-suppressive soils. PMID:22913725

  13. Codon usage bias in phylum Actinobacteria: relevance to environmental adaptation and host pathogenicity.

    PubMed

    Lal, Devi; Verma, Mansi; Behura, Susanta K; Lal, Rup

    2016-10-01

    Actinobacteria are Gram-positive bacteria commonly found in soil, freshwater and marine ecosystems. In this investigation, bias in codon usages of ninety actinobacterial genomes was analyzed by estimating different indices of codon bias such as Nc (effective number of codons), SCUO (synonymous codon usage order), RSCU (relative synonymous codon usage), as well as sequence patterns of codon contexts. The results revealed several characteristic features of codon usage in Actinobacteria, as follows: 1) C- or G-ending codons are used frequently in comparison with A- and U ending codons; 2) there is a direct relationship of GC content with use of specific amino acids such as alanine, proline and glycine; 3) there is an inverse relationship between GC content and Nc estimates, 4) there is low SCUO value (<0.5) for most genes; and 5) GCC-GCC, GCC-GGC, GCC-GAG and CUC-GAC are the frequent context sequences among codons. This study highlights the fact that: 1) in Actinobacteria, extreme GC content and codon bias are driven by mutation rather than natural selection; (2) traits like aerobicity are associated with effective natural selection and therefore low GC content and low codon bias, demonstrating the role of both mutational bias and translational selection in shaping the habitat and phenotype of actinobacterial species.

  14. Efficacy of protease inhibitor from marine Streptomyces sp. VITBVK2 against Leishmania donovani - An in vitro study.

    PubMed

    Sreedharan, Veena; Bhaskara Rao, K V

    2017-03-01

    In the present study the leishmanicidal effect of potential protease inhibitor producing marine actinobacterial isolate has been investigated against Leishmania donovani, the causative agent of visceral leishmaniasis. Among 89 marine actinobacteria isolated from a salt pan in Kanyakumari, only one isolate (BVK2) showed 97% of protease inhibition activity against trypsin. Moderate to high protease inhibitor activity was shown by isolate BVK2 on proteinase (30%) and chymotrypsin (85%). In optimization study for protease inhibitor production glucose as carbon source and casein as nitrogen source showed the best activity. In the in-vitro Fluorescence-activated cell sorting (FACS) assay, 100 μg/ml of BVK2 extract was active against amastigotes in infected J774A.1 macrophages and showed 87% of parasitic inhibition. The isolate BVK2 showed significant anti-parasitic activity with an IC50 of 27.1 μg/ml after double doses were administered. The potential isolate was identified by molecular 16S rRNA gene sequencing as Streptomyces sp. VITBVK2. The results obtained suggest that the marine actinobacterial extract which have novel metabolites can be considered as a potential source for the development of drugs.

  15. Marine actinobacteria associated with marine organisms and their potentials in producing pharmaceutical natural products.

    PubMed

    Valliappan, Karuppiah; Sun, Wei; Li, Zhiyong

    2014-09-01

    Actinobacteria are ubiquitous in the marine environment, playing an important ecological role in the recycling of refractory biomaterials and producing novel natural products with pharmic applications. Actinobacteria have been detected or isolated from the marine creatures such as sponges, corals, mollusks, ascidians, seaweeds, and seagrass. Marine organism-associated actinobacterial 16S rRNA gene sequences, i.e., 3,003 sequences, deposited in the NCBI database clearly revealed enormous numbers of actinobacteria associated with marine organisms. For example, RDP classification of these sequences showed that 112 and 62 actinobacterial genera were associated with the sponges and corals, respectively. In most cases, it is expected that these actinobacteria protect the host against pathogens by producing bioactive compounds. Natural products investigation and functional gene screening of the actinobacteria associated with the marine organisms revealed that they can synthesize numerous natural products including polyketides, isoprenoids, phenazines, peptides, indolocarbazoles, sterols, and others. These compounds showed anticancer, antimicrobial, antiparasitic, neurological, antioxidant, and anti-HIV activities. Therefore, marine organism-associated actinobacteria represent an important resource for marine drugs. It is an upcoming field of research to search for novel actinobacteria and pharmaceutical natural products from actinobacteria associated with the marine organisms. In this review, we attempt to summarize the present knowledge on the diversity and natural products production of actinobacteria associated with the marine organisms, based on the publications from 1991 to 2013.

  16. Deciphering the Genome of Polyphosphate Accumulating Actinobacterium Microlunatus phosphovorus

    PubMed Central

    Kawakoshi, Akatsuki; Nakazawa, Hidekazu; Fukada, Junji; Sasagawa, Machi; Katano, Yoko; Nakamura, Sanae; Hosoyama, Akira; Sasaki, Hiroki; Ichikawa, Natsuko; Hanada, Satoshi; Kamagata, Yoichi; Nakamura, Kazunori; Yamazaki, Shuji; Fujita, Nobuyuki

    2012-01-01

    Polyphosphate accumulating organisms (PAOs) belong mostly to Proteobacteria and Actinobacteria and are quite divergent. Under aerobic conditions, they accumulate intracellular polyphosphate (polyP), while they typically synthesize polyhydroxyalkanoates (PHAs) under anaerobic conditions. Many ecological, physiological, and genomic analyses have been performed with proteobacterial PAOs, but few with actinobacterial PAOs. In this study, the whole genome sequence of an actinobacterial PAO, Microlunatus phosphovorus NM-1T (NBRC 101784T), was determined. The number of genes for polyP metabolism was greater in M. phosphovorus than in other actinobacteria; it possesses genes for four polyP kinases (ppks), two polyP-dependent glucokinases (ppgks), and three phosphate transporters (pits). In contrast, it harbours only a single ppx gene for exopolyphosphatase, although two copies of ppx are generally present in other actinobacteria. Furthermore, M. phosphovorus lacks the phaABC genes for PHA synthesis and the actP gene encoding an acetate/H+ symporter, both of which play crucial roles in anaerobic PHA accumulation in proteobacterial PAOs. Thus, while the general features of M. phosphovorus regarding aerobic polyP accumulation are similar to those of proteobacterial PAOs, its anaerobic polyP use and PHA synthesis appear to be different. PMID:22923697

  17. Genomics of Actinobacteria: Tracing the Evolutionary History of an Ancient Phylum†

    PubMed Central

    Ventura, Marco; Canchaya, Carlos; Tauch, Andreas; Chandra, Govind; Fitzgerald, Gerald F.; Chater, Keith F.; van Sinderen, Douwe

    2007-01-01

    Summary: Actinobacteria constitute one of the largest phyla among Bacteria and represent gram-positive bacteria with a high G+C content in their DNA. This bacterial group includes microorganisms exhibiting a wide spectrum of morphologies, from coccoid to fragmenting hyphal forms, as well as possessing highly variable physiological and metabolic properties. Furthermore, Actinobacteria members have adopted different lifestyles, and can be pathogens (e.g., Corynebacterium, Mycobacterium, Nocardia, Tropheryma, and Propionibacterium), soil inhabitants (Streptomyces), plant commensals (Leifsonia), or gastrointestinal commensals (Bifidobacterium). The divergence of Actinobacteria from other bacteria is ancient, making it impossible to identify the phylogenetically closest bacterial group to Actinobacteria. Genome sequence analysis has revolutionized every aspect of bacterial biology by enhancing the understanding of the genetics, physiology, and evolutionary development of bacteria. Various actinobacterial genomes have been sequenced, revealing a wide genomic heterogeneity probably as a reflection of their biodiversity. This review provides an account of the recent explosion of actinobacterial genomics data and an attempt to place this in a biological and evolutionary context. PMID:17804669

  18. Littoral lichens as a novel source of potentially bioactive Actinobacteria

    PubMed Central

    Parrot, Delphine; Antony-Babu, Sanjay; Intertaglia, Laurent; Grube, Martin; Tomasi, Sophie; Suzuki, Marcelino T.

    2015-01-01

    Cultivable Actinobacteria are the largest source of microbially derived bioactive molecules. The high demand for novel antibiotics highlights the need for exploring novel sources of these bacteria. Microbial symbioses with sessile macro-organisms, known to contain bioactive compounds likely of bacterial origin, represent an interesting and underexplored source of Actinobacteria. We studied the diversity and potential for bioactive-metabolite production of Actinobacteria associated with two marine lichens (Lichina confinis and L. pygmaea; from intertidal and subtidal zones) and one littoral lichen (Roccella fuciformis; from supratidal zone) from the Brittany coast (France), as well as the terrestrial lichen Collema auriforme (from a riparian zone, Austria). A total of 247 bacterial strains were isolated using two selective media. Isolates were identified and clustered into 101 OTUs (98% identity) including 51 actinobacterial OTUs. The actinobacterial families observed were: Brevibacteriaceae, Cellulomonadaceae, Gordoniaceae, Micrococcaceae, Mycobacteriaceae, Nocardioidaceae, Promicromonosporaceae, Pseudonocardiaceae, Sanguibacteraceae and Streptomycetaceae. Interestingly, the diversity was most influenced by the selective media rather than lichen species or the level of lichen thallus association. The potential for bioactive-metabolite biosynthesis of the isolates was confirmed by screening genes coding for polyketide synthases types I and II. These results show that littoral lichens are a source of diverse potentially bioactive Actinobacteria. PMID:26514347

  19. Multi-functional nano silver: A novel disruptive and theranostic agent for pathogenic organisms in real-time

    PubMed Central

    Gopinath, Ponnusamy Manogaran; Ranjani, Anandan; Dhanasekaran, Dharumadurai; Thajuddin, Nooruddin; Archunan, Govindaraju; Akbarsha, Mohammad Abdulkader; Gulyás, Balázs; Padmanabhan, Parasuraman

    2016-01-01

    The present study was aimed at evaluating the fluorescence property, sporicidal potency against Bacillus and Clostridium endospores, and surface disinfecting ability of biogenic nano silver. The nano silver was synthesized using an actinobacterial cell-filtrate. The fluorescence property as well as imaging facilitator potency of this nano silver was verified adopting spectrofluorometer along with fluorescent and confocal laser scanning microscope wherein strong emission and bright green fluorescence, respectively, on the entire spore surface was observed. Subsequently, the endospores of B. subtilis, B. cereus, B. amyloliquefaciens, C. perfringens and C. difficile were treated with physical sporicides, chemical sporicides and nano silver, in which the nano silver brought about pronounced inhibition even at a very low concentration. Finally, the environmental surface-sanitizing potency of nano silver was investigated adopting cage co-contamination assay, wherein vital organs of mice exposed to the nano silver-treated cage did not show any signs of pathological lesions, thus signifying the ability of nano silver to completely disinfect the spore or reduce the count required for infection. Taken these observations together, we have shown the multi-functional biological properties of the nano silver, synthesized using an actinobacterial cell-filtrate, which could be of application in advanced diagnostics, biomedical engineering and therapeutics in the near future. PMID:27666290

  20. An airborne actinobacteria Nocardiopsis alba isolated from bioaerosol of a mushroom compost facility.

    PubMed

    Paściak, Mariola; Pawlik, Krzysztof; Gamian, Andrzej; Szponar, Bogumiła; Skóra, Justyna; Gutarowska, Beata

    2014-01-01

    Actinobacteria are widely distributed in many environments and represent the most important trigger to the occupant respiratory health. Health complaints, including hypersensitivity pneumonitis of the workers, were recorded in a mushroom compost facility (MCF). The studies on the airborne bacteria were carried out to find a possible microbiological source of these symptoms. Culture analysis of compost bioaerosols collected in different location of the MCF was performed. An assessment of the indoor microbial exposure revealed bacterial flora of bioaerosol in the mushroom compost facility represented by Bacillus, Geobacillus, Micrococcus, Pseudomonas, Staphylococcus spp., and actinobacterial strain with white aerial mycelium. The thermotolerant actinobacterial strain of the same morphology was repeatedly isolated from many locations in MCF: air, compost sample, and solid surface in production hall. On the base of complex morphological, chemotaxonomic, and phylogenetic characteristics, the isolate has been classified as Nocardiopsis alba. Dominant position of N. alba in microbial environment of the mushroom compost facility may represent an indicator microorganism in compost bioaerosol. The bioavailability of N. alba in mushroom compost facility creates potential risk for the health of workers, and the protection of respiratory tract and/or skin is strongly recommended.

  1. Marine Actinobacteria from the Gulf of California: diversity, abundance and secondary metabolite biosynthetic potential

    PubMed Central

    Becerril-Espinosa, Amayaly; Freel, Kelle C.; Jensen, Paul R.

    2015-01-01

    The Gulf of California is a coastal marine ecosystem characterized as having abundant biological resources and a high level of endemism. In this work we report the isolation and characterization of Actinobacteria from different sites in the western Gulf of California. We collected 126 sediment samples and isolated on average 3.1–38.3 Actinobacterial strains from each sample. Phylogenetic analysis of 136 strains identified them as members of the genera Actinomadura, Micromonospora, Nocardiopsis, Nonomuraea, Saccharomonospora, Salinispora, Streptomyces and Verrucosispora. These strains were grouped into 26–56 operational taxonomic units (OTUs) based on 16S rRNA gene sequence identities of 98–100 %. At 98 % sequence identity, three OTUs appear to represent new taxa while nine (35 %) have only been reported from marine environments. Sixty-three strains required seawater for growth. These fell into two OTUs at the 98 % identity level and include one that failed to produce aerial hyphae and was only distantly related (≤95.5 % 16S identity) to any previously cultured Streptomyces sp. Phylogenetic analyses of ketosynthase domains associated with polyketide synthase genes revealed sequences that ranged from 55 to 99 % nucleotide identity to experimentally characterized biosynthetic pathways suggesting that some may be associated with the production of new secondary metabolites. These results indicate that marine sediments from the Gulf of California harbor diverse Actinobacterial taxa with the potential to produce new secondary metabolites. PMID:23229438

  2. Vitamin supplementation by gut symbionts ensures metabolic homeostasis in an insect host

    PubMed Central

    Salem, Hassan; Bauer, Eugen; Strauss, Anja S.; Vogel, Heiko; Marz, Manja; Kaltenpoth, Martin

    2014-01-01

    Despite the demonstrated functional importance of gut microbes, our understanding of how animals regulate their metabolism in response to nutritionally beneficial symbionts remains limited. Here, we elucidate the functional importance of the African cotton stainer's (Dysdercus fasciatus) association with two actinobacterial gut symbionts and subsequently examine the insect's transcriptional response following symbiont elimination. In line with bioassays demonstrating the symbionts' contribution towards host fitness through the supplementation of B vitamins, comparative transcriptomic analyses of genes involved in import and processing of B vitamins revealed an upregulation of gene expression in aposymbiotic (symbiont-free) compared with symbiotic individuals; an expression pattern that is indicative of B vitamin deficiency in animals. Normal expression levels of these genes, however, can be restored by either artificial supplementation of B vitamins into the insect's diet or reinfection with the actinobacterial symbionts. Furthermore, the functional characterization of the differentially expressed thiamine transporter 2 through heterologous expression in Xenopus laevis oocytes confirms its role in cellular uptake of vitamin B1. These findings demonstrate that despite an extracellular localization, beneficial gut microbes can be integral to the host's metabolic homeostasis, reminiscent of bacteriome-localized intracellular mutualists. PMID:25339726

  3. Marine Actinobacteria as a source of compounds for phytopathogen control: An integrative metabolic-profiling / bioactivity and taxonomical approach

    PubMed Central

    Betancur, Luz A.; Naranjo-Gaybor, Sandra J.; Vinchira-Villarraga, Diana M.; Moreno-Sarmiento, Nubia C.; Maldonado, Luis A.; Suarez-Moreno, Zulma R.; Acosta-González, Alejandro; Padilla-Gonzalez, Gillermo F.; Puyana, Mónica; Castellanos, Leonardo; Ramos, Freddy A.

    2017-01-01

    Marine bacteria are considered as promising sources for the discovery of novel biologically active compounds. In this study, samples of sediment, invertebrate and algae were collected from the Providencia and Santa Catalina coral reef (Colombian Caribbean Sea) with the aim of isolating Actinobateria-like strain able to produce antimicrobial and quorum quenching compounds against pathogens. Several approaches were used to select actinobacterial isolates, obtaining 203 strains from all samples. According to their 16S rRNA gene sequencing, a total of 24 strains was classified within Actinobacteria represented by three genera: Streptomyces, Micromonospora, and Gordonia. In order to assess their metabolic profiles, the actinobacterial strains were grown in liquid cultures, and LC-MS-based analyses from ethyl acetate fractions were performed. Based on taxonomical classification, screening information of activity against phytopathogenic strains and quorum quenching activity, as well as metabolic profiling, six out of the 24 isolates were selected for follow-up with chemical isolation and structure identification analyses of putative metabolites involved in antimicrobial activities. PMID:28225766

  4. Multi-functional nano silver: A novel disruptive and theranostic agent for pathogenic organisms in real-time.

    PubMed

    Gopinath, Ponnusamy Manogaran; Ranjani, Anandan; Dhanasekaran, Dharumadurai; Thajuddin, Nooruddin; Archunan, Govindaraju; Akbarsha, Mohammad Abdulkader; Gulyás, Balázs; Padmanabhan, Parasuraman

    2016-09-26

    The present study was aimed at evaluating the fluorescence property, sporicidal potency against Bacillus and Clostridium endospores, and surface disinfecting ability of biogenic nano silver. The nano silver was synthesized using an actinobacterial cell-filtrate. The fluorescence property as well as imaging facilitator potency of this nano silver was verified adopting spectrofluorometer along with fluorescent and confocal laser scanning microscope wherein strong emission and bright green fluorescence, respectively, on the entire spore surface was observed. Subsequently, the endospores of B. subtilis, B. cereus, B. amyloliquefaciens, C. perfringens and C. difficile were treated with physical sporicides, chemical sporicides and nano silver, in which the nano silver brought about pronounced inhibition even at a very low concentration. Finally, the environmental surface-sanitizing potency of nano silver was investigated adopting cage co-contamination assay, wherein vital organs of mice exposed to the nano silver-treated cage did not show any signs of pathological lesions, thus signifying the ability of nano silver to completely disinfect the spore or reduce the count required for infection. Taken these observations together, we have shown the multi-functional biological properties of the nano silver, synthesized using an actinobacterial cell-filtrate, which could be of application in advanced diagnostics, biomedical engineering and therapeutics in the near future.

  5. Marine Actinobacteria as a source of compounds for phytopathogen control: An integrative metabolic-profiling / bioactivity and taxonomical approach.

    PubMed

    Betancur, Luz A; Naranjo-Gaybor, Sandra J; Vinchira-Villarraga, Diana M; Moreno-Sarmiento, Nubia C; Maldonado, Luis A; Suarez-Moreno, Zulma R; Acosta-González, Alejandro; Padilla-Gonzalez, Gillermo F; Puyana, Mónica; Castellanos, Leonardo; Ramos, Freddy A

    2017-01-01

    Marine bacteria are considered as promising sources for the discovery of novel biologically active compounds. In this study, samples of sediment, invertebrate and algae were collected from the Providencia and Santa Catalina coral reef (Colombian Caribbean Sea) with the aim of isolating Actinobateria-like strain able to produce antimicrobial and quorum quenching compounds against pathogens. Several approaches were used to select actinobacterial isolates, obtaining 203 strains from all samples. According to their 16S rRNA gene sequencing, a total of 24 strains was classified within Actinobacteria represented by three genera: Streptomyces, Micromonospora, and Gordonia. In order to assess their metabolic profiles, the actinobacterial strains were grown in liquid cultures, and LC-MS-based analyses from ethyl acetate fractions were performed. Based on taxonomical classification, screening information of activity against phytopathogenic strains and quorum quenching activity, as well as metabolic profiling, six out of the 24 isolates were selected for follow-up with chemical isolation and structure identification analyses of putative metabolites involved in antimicrobial activities.

  6. Descending into the abyss: Bathymetric patterns of diversity in decapod crustaceans shift with taxonomic level and life strategies

    NASA Astrophysics Data System (ADS)

    Rosa, Rui; Boavida-Portugal, Joana; Trübenbach, Katja; Baptista, Miguel; Araújo, Ricardo; Calado, Ricardo

    2012-06-01

    The aim of this study was to examine the depth-related changes in the diversity of decapod crustaceans from the intertidal to abyssal zones off Madeira Archipelago, a chain of islands in the subtropical North East Atlantic Ocean. The bathymetric gradient in species richness was evaluated using the reported ranges of 175 out of approximately 186 decapod species known in this archipelago. The depth-related changes at different taxonomic (order, sub-orders and families) and life strategy (pelagic, benthopelagic and benthic) levels were investigated and different ecological hypotheses (species-energy, mid-domain and Rapoport's effects) were tested to explain the observed patterns. No unimodal trend of Decapoda diversity was revealed and, instead, a monotonic decrease towards the abyss was observed, mainly as a consequence of the depth-related changes in the benthic diversity of the suborder Pleocyemata. Nonetheless, all bathymetric gradients of pelagic diversity (at order and suborder levels) displayed parabolic trends. There was also a general increase in bathymetric range towards greater depth, and the major faunal break was identified within the continental shelf area. All species richness-depth patterns were significantly nested, but there was a clear increasing trend in randomness from the benthic to the pelagic realm. The present study shows for the first time that even within the same taxonomic group and geographic region different bathymetric patterns of diversity can be observed, depending on the taxonomic level and, more importantly, on the group's life strategies. Moreover, our analysis supports the species-energy hypothesis, implicating a combination of temperature and food availability as the main causal predictors explaining diversity variation.

  7. Sequence alignment of 18S ribosomal RNA and the basal relationships of Adephagan beetles: evidence for monophyly of aquatic families and the placement of Trachypachidae.

    PubMed

    Shull, V L; Vogler, A P; Baker, M D; Maddison, D R; Hammond, P M

    2001-01-01

    Current hypotheses regarding family relationships in the suborder Adephaga (Coleoptera) are conflicting. Here we report full-length 18S ribosomal RNA sequences of 39 adephagans and 13 outgroup taxa. Data analysis focused on the impact of sequence alignment on tree topology, using two principally different approaches. Tree alignments, which seek to minimize indels and substitutions on the tree in a single step, as implemented in an approximate procedure by the computer program POY, were contrasted with a more traditional procedure based on alignments followed by phylogenetic inference based on parsimony, likelihood, and distance analyses. Despite substantial differences between the procedures, phylogenetic conclusions regarding basal relationships within Adephaga and relationships between the four suborders of Coleoptera were broadly similar. The analysis weakly supports monophyly of Adephaga, with Polyphaga usually as its sister, and the two small suborders Myxophaga and Archostemata basal to them. In some analyses, however, Polyphaga was reconstructed as having arisen from within Hydradephaga. Adephaga generally split into two monophyletic groups, corresponding to the terrestrial Geadephaga and the aquatic Hydradephaga, as initially proposed by Crowson in 1955, consistent with a single colonization of the aquatic environment by adephagan ancestors and contradicting the recent proposition of three independent invasions. A monophyletic Hydradephaga is consistently, though not strongly, supported under most analyses, and a parametric bootstrapping test significantly rejects an hypothesis of nonmonophyly. The enigmatic Trachypachidae, which exhibit many similarities to aquatic forms but whose species are entirely terrestrial, were usually recovered as a basal lineage within Geadephaga. Strong evidence opposes the view that terrestrial trachypachids are related to the dytiscoid water beetles.

  8. A six-year study of insect emergence from temporary flooded wetlands in central Sweden, with and without Bti-based mosquito control.

    PubMed

    Persson Vinnersten, T Z; Lundström, J O; Schäfer, M L; Petersson, E; Landin, J

    2010-12-01

    In temporary wetlands in the River Dalälven floodplains, recurrent but irregular floods induce massive hatching of the flood-water mosquito Aedes sticticus, which causes enormous nuisance. Flood-water mosquito control using the biological larvicide Bacillus thuringiensis var. israelensis (Bti) was commenced in parts of the floodplains during 2002, and here we report the first six years of full-season monitoring of general insect emergence from temporary wetlands with and without treatment. Emergence traps, which were emptied weekly, were used from May to September each year. A total of 137,153 insects of 13 taxonomic orders were collected. Diptera was highly dominating and especially the sub-order Nematocera with 18 families was a very prominent taxon. Bti-treatment effects were analysed by taxonomic order, by sub-order in Diptera and Hemiptera, and by family for Nematocera and Coleoptera for the whole study period. We found no significant negative effects of Bti treatments on the production of insects by taxonomic order, with the exception of Coleoptera in the long term. However, no significant negative effects were found for the Coleoptera families, neither in the short term nor in the long term. There was no significant negative treatment effect on Nematocera production, neither when analyzed for the whole sub-order nor when analyzed by family. However, abundance of Ceratopogonidae was significantly higher in experimental than in reference wetlands. We conclude that Bti-treatment effects on insect production may be minute in comparison to other environmental factors structuring the insect fauna of the temporary wetlands studied.

  9. Complete mitochondrial genome of the Eurasian flying squirrel Pteromys volans (Sciuromorpha, Sciuridae) and revision of rodent phylogeny.

    PubMed

    Ryu, Shi Hyun; Kwak, Min Jung; Hwang, Ui Wook

    2013-02-01

    In this study, the complete mitochondrial genome of the Eurasian flying squirrel Pteromys volans (Rodentia, Sciuromorpha, Sciuridae) was sequenced and characterized in detail. The entire mitochondrial genome of P. volans consisted of 16,513 bp and contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two non-coding regions. Its gene arrangement pattern was consistent with the mammalian ground pattern. The overall base composition and AT contents were similar to those of other rodent mitochondrial genomes. The light-strand origin generally identified between tRNA ( Asn ) and tRNA ( Cys ) consisted of a secondary structure with an 11-bp stem and an 11-bp loop. The large control region was constructed of three characteristic domains, ETAS, CD, and CSB without any repeat sequences. Each domain contained ETAS1, subsequences A, B, and C, and CSB1, respectively. In order to examine phylogenetic contentious issues of the monophyly of rodents and phylogenetic relationships among five rodent suborders, here, phylogenetic analyses based on nucleotide sequence data of the 35 rodent and 3 lagomorph mitochondrial genomes were performed using the Bayesian inference and maximum likelihood method. The result strongly supported the rodent monophyly with high node confidence values (BP 100 % in ML and BPP 1.00 in BI) and also monophylies of four rodent suborders (BP 85-100 % in ML and BPP 1.00 in BI), except for Anomalumorpha in which only one species was examined here. Also, phylogenetic relationships among the five rodent suborders were suggested and discussed in detail.

  10. First identifiable Mesozoic harvestman (Opiliones: Dyspnoi) from Cretaceous Burmese amber.

    PubMed

    Giribet, Gonzalo; Dunlop, Jason A

    2005-05-22

    Two inclusions in a piece of Upper Cretaceous (Albian) Burmese amber from Myanmar are described as a harvestman (Arachnida: Opiliones), Halitherses grimaldii new genus and species. The first Mesozoic harvestman to be named can be referred to the suborder Dyspnoi for the following reasons: prosoma divided into two regions, the posterior formed by the fusion of the meso- and metapeltidium; palp lacking a terminal claw, with clavate setae, and tarsus considerably shorter than the tibia. The bilobed, anteriorly projecting ocular tubercle is reminiscent of that of ortholasmatine nemastomatids. The status of other Mesozoic fossils referred to Opiliones is briefly reviewed.

  11. G-banded karotype and ideogram for the critically endangered North Atlantic right whale (Eubalanea glacialis)

    USGS Publications Warehouse

    Pause, K.C.; Bonde, R.K.; McGuire, P.M.; Zori, Roberto T.; Gray, B.A.

    2006-01-01

    Published cytogenetic data for extant cetacean species remain incomplete. In a review of the literature, we found karyotypic information for 6 of the 13 tentatively recognized species of the suborder Mysticeti (baleen whales). Among those yet to be described is the critically endangered North Atlantic right whale (Eubalaena glacialis). Herein, we describe and propose a first-generation G-banded karyotype and ideogram for this species (2n = 42), obtained from peripheral blood chromosome preparations from a stranded male calf. This information may prove useful for future genetic mapping projects and for interspecific and intraspecific genomic comparisons by techniques such as zoo-FISH.

  12. The Identification of Octocorals from the Northern Region of Straits of Malacca

    PubMed Central

    Mohammad, Mahadi; Apandi, Zaharatul Naa’imah; Marican, Hana Abdul Wahab; Kamphol, Nadthikphorn; Mubin, Nur Ain Amani Abdul; Salleh, Sazlina; Ismail, Md Nizam

    2016-01-01

    Coral reefs in the northern region of the Straits of Malacca have a diverse group of octocorals growing on its bed. The octocorals identified in this study are from islands along the Straits. In this study, 23 specimens were identified, belonging to 4 sub-orders, which have been subdivided into 8 families. From these 8 families, 15 different genera have been identified. The identification process for this research was conducted based on five important keys; the external form and colouration, polyps or colonial and fundamental structure of colonies, monomorphic or dimorphic, the arrangement of polyps, and the arrangement of sclerites. PMID:27965745

  13. Cloning and sequencing of dolphinfish (Coryphaena hippurus, Coryphaenidae) growth hormone-encoding cDNA.

    PubMed

    Peduel, A D; Elizur, A; Knibb, W

    1994-01-01

    The cDNA encoding the preprotein growth hormone from the dolphinfish (Coryphaena hippurus) has been cloned and sequenced. The cDNA was derived by reverse transcription of RNA from the pituitary of a young fish using the method known as Rapid Amplification of cDNA Ends (RACE). An oligonucleotide primer corresponding to the 5' region of Pagrus major and the universal RACE primer enabled amplification using the Polymerase Chain Reaction (PCR). The dolphinfish and yellow-tail, Seriola quineqeradiata, are both members of the sub-order Percoidei (Perciforme) and their GH sequences show a high level of homology.

  14. Phylogenetic relationships and a new classification of the family Cyclopteridae (Perciformes: Cottoidei).

    PubMed

    Oku, Kanami; Imamura, Hisashi; Yabe, Mamoru

    2017-01-16

     Phylogenetic relationships of the family Cyclopteridae were reconstructed based on osteological and external characters.  The monophyly of the family was strongly supported by 47 commonly recognized synapomorphies, including six autapomorphies (plus one additional autapomorphy, presence of a dorsal process on the pelvis, recognized after the phylogenetic analysis) among the suborder Cottoidei.  As a result of the cladistic analysis, a single most parsimonious phylogeny was obtained, based on characters in 32 transformation series.  A new classification of Cyclopteridae based on reconstructed relationships, including three subfamilies [Liparopsinae, Cyclopterinae and Eumicrotreminae (newly established)] and four genera (Aptocyclus, Cyclopsis, Cyclopterus and Eumicrotremus), is proposed.

  15. Genome sequence of a crustacean iridovirus, IIV31, isolated from the pill bug, Armadillidium vulgare.

    PubMed

    Piégu, Benoît; Guizard, Sébastien; Yeping, Tan; Cruaud, Corinne; Asgari, Sassan; Bideshi, Dennis K; Federici, Brian A; Bigot, Yves

    2014-07-01

    Members of the family Iridoviridae are animal viruses that infect only invertebrates and poikilothermic vertebrates. The invertebrate iridovirus 31 (IIV31) was originally isolated from adult pill bugs, Armadillidium vulgare (class Crustacea, order Isopoda, suborder Oniscidea), found in southern California on the campus of the University of California, Riverside, USA. IIV31 virions are icosahedral, have a diameter of about 135 nm, and contain a dsDNA genome 220.222 kbp in length, with 35.09 mol % G+C content and 203 ORFs. Here, we describe the complete genome sequence of this virus and its annotation. This is the eighth genome sequence of an IIV reported.

  16. Analyses of mitochondrial genomes strongly support a hippopotamus-whale clade.

    PubMed

    Ursing, B M; Arnason, U

    1998-12-07

    Although the sister-group relationship between Cetacea and Artiodactyla is widely accepted, the actual artiodactyl group which is closest to Cetacea has not been conclusively identified. In the present study, we have sequenced the complete mitochondrial genome of the hippopotamus, Hippopotamus amphibius, and included it in phylogenetic analyses together with 15 other placental mammals. These analyses separated the hippopotamus from the other suiform included, the pig, and identified the hippopotamus as the artiodactyl sister group of the cetaceans, thereby making both. Artiodactyla and the suborder. Suiformes paraphyletic. The divergence between the hippopotamid and cetacean lineages was calculated using this molecular data and was estimated at ca. 54 Ma BP.

  17. Evolutionary history of anglerfishes (Teleostei: Lophiiformes): a mitogenomic perspective

    PubMed Central

    2010-01-01

    Background The teleost order Lophiiformes, commonly known as the anglerfishes, contains a diverse array of marine fishes, ranging from benthic shallow-water dwellers to highly modified deep-sea midwater species. They comprise 321 living species placed in 68 genera, 18 families and 5 suborders, but approximately half of the species diversity is occupied by deep-sea ceratioids distributed among 11 families. The evolutionary origins of such remarkable habitat and species diversity, however, remain elusive because of the lack of fresh material for a majority of the deep-sea ceratioids and incompleteness of the fossil record across all of the Lophiiformes. To obtain a comprehensive picture of the phylogeny and evolutionary history of the anglerfishes, we assembled whole mitochondrial genome (mitogenome) sequences from 39 lophiiforms (33 newly determined during this study) representing all five suborders and 17 of the 18 families. Sequences of 77 higher teleosts including the 39 lophiiform sequences were unambiguously aligned and subjected to phylogenetic analysis and divergence time estimation. Results Partitioned maximum likelihood analysis confidently recovered monophyly for all of the higher taxa (including the order itself) with the exception of the Thaumatichthyidae (Lasiognathus was deeply nested within the Oneirodidae). The mitogenomic trees strongly support the most basal and an apical position of the Lophioidei and a clade comprising Chaunacoidei + Ceratioidei, respectively, although alternative phylogenetic positions of the remaining two suborders (Antennarioidei and Ogcocephaloidei) with respect to the above two lineages are statistically indistinguishable. While morphology-based intra-subordinal relationships for relatively shallow, benthic dwellers (Lophioidei, Antennarioidei, Ogcocephaloidei, Chaunacoidei) are either congruent with or statistically indistinguishable from the present mitogenomic tree, those of the principally deep-sea midwater dwellers

  18. Complete mitochondrial genome of Amolops mantzorum (Anura: Ranidae).

    PubMed

    Shan, Xiang; Xia, Yun; Kakehashi, Ryosuke; Kurabayashi, Atsushi; Zou, Fang-Dong; Zeng, Xiao-Mao

    2016-01-01

    Sichuan torrent frog, Amolops mantzorum (family Ranidae, suborder Neobatrachia), possesses heteromorphic sex chromosomes unusual characteristics among amphibians. We determined the complete nucleotide sequence of the A. mantzorum mitogenome. This genome is 17,744 bp in length and contains 37 genes, 1 control region, and 1 light strand replication origin typically found in vertebrate mtDNAs. In the A. mantzorum mitogenome, a novel gene arrangement is observed within the WANCY tRNA gene cluster region. This mt gene arrangement seems to be usable as a molecular maker to distinguish to this species from other species in the genus Amolops.

  19. [Genosystematics and new insight on phylogeny and taxonomy of liverworts].

    PubMed

    Vil'net, A A; Konstantinova, N A; Troitskiĭ, A V

    2009-01-01

    The paper covers a current state of molecular studies of liverworts including new data from authors. The traditional conceptions of liverwort phylogeny and systematics were changed greatly in a result of recent molecular researches. The phylogenetic inferences from studies of different DNA loci and species sampling are mainly congruent. The phylogeny and systematics of one of the largest and taxonomically difficult suborder Jungermaniineae was discussed based on analyses of internal transcribed spacer ITS1-2 of nuclear rDNA and chloroplast trnL-F of large species number.

  20. World Checklist of Opiliones species (Arachnida). Part 2: Laniatores – Samooidea, Zalmoxoidea and Grassatores incertae sedis

    PubMed Central

    Souza, Daniele R.; Pérez-González, Abel

    2015-01-01

    Abstract Including more than 6500 species, Opiliones is the third most diverse order of Arachnida, after the megadiverse Acari and Araneae. This database is part 2 of 12 of a project containing an intended worldwide checklist of species and subspecies of Opiliones, and it includes the members of the suborder Laniatores, infraorder Grassatores of the superfamilies Samooidea and Zalmoxoidea plus the genera currently not allocated to any family (i.e. Grassatores incertae sedis). In this Part 2, a total of 556 species and subspecies are listed. PMID:26752965

  1. Diversity of Culturable Thermophilic Actinobacteria in Hot Springs in Tengchong, China and Studies of their Biosynthetic Gene Profiles.

    PubMed

    Liu, Lan; Salam, Nimaichand; Jiao, Jian-Yu; Jiang, Hong-Chen; Zhou, En-Min; Yin, Yi-Rui; Ming, Hong; Li, Wen-Jun

    2016-07-01

    The class Actinobacteria has been a goldmine for the discovery of antibiotics and has attracted interest from both academics and industries. However, an absence of novel approaches during the last few decades has limited the discovery of new microbial natural products useful for industries. Scientists are now focusing on the ecological aspects of diverse environments including unexplored or underexplored habitats and extreme environments in the search for new metabolites. This paper reports on the diversity of culturable actinobacteria associated with hot springs located in Tengchong County, Yunnan Province, southwestern China. A total of 58 thermophilic actinobacterial strains were isolated from the samples collected from ten hot springs distributed over three geothermal fields (e.g., Hehua, Rehai, and Ruidian). Phylogenetic positions and their biosynthetic profiles were analyzed by sequencing 16S rRNA gene and three biosynthetic gene clusters (KS domain of PKS-I, KSα domain of PKS-II and A domain of NRPS). On the basis of 16S rRNA gene phylogenetic analysis, the 58 strains were affiliated with 12 actinobacterial genera: Actinomadura Micromonospora, Microbispora, Micrococcus, Nocardiopsis, Nonomuraea, Promicromonospora, Pseudonocardia, Streptomyces, Thermoactinospora, Thermocatellispora, and Verrucosispora, of which the two novel genera Thermoactinospora and Thermocatellisopora were recently described from among these strains. Considering the biosynthetic potential of these actinobacterial strains, 22 were positive for PCR amplification of at least one of the three biosynthetic gene clusters (PKS-I, PKS-II, and NRPS). These actinobacteria were further subjected to antimicrobial assay against five opportunistic human pathogens (Acinetobacter baumannii, Escherichia coli, Micrococcus luteus, Staphylococcus aureus and Streptococcus faecalis). All of the 22 strains that were positive for PCR amplification of at least one of the biosynthetic gene domains exhibited

  2. Phylogeny and evolution of life history strategies of the parasitic barnacles (Crustacea, Cirripedia, Rhizocephala).

    PubMed

    Glenner, Henrik; Hebsgaard, Martin Bay

    2006-12-01

    The barnacles (Crustacea, Cirripedia) consist of three well-defined orders: the conventional filter-feeding barnacles (Thoracica), the burrowing barnacles (Acrothoracica), and the parasitic barnacles (Rhizocephala). Thoracica and Acrothoracica feed by catching food particles from the surrounding seawater using their thoracic appendages while members of Rhizocephala are exclusively parasitic. The parasite consists of a sac-shaped, external reproductive organ situated on the abdomen of its crustacean host and a nutrient-absorbing root system embedded into the heamolymph of the host. In order to resolve the phylogenetic relationship of the order Rhizocephala and elucidate the evolution of the different life history strategies found within the Rhizocephala, we have performed the first comprehensive phylogenetic analysis of the group. Our results indicate that Rhizocephala is monophyletic with a filter-feeding barnacle-like ancestor. The host-infective stage, the kentrogon larva, inserted in the lifecycle of the rhizocephalan suborder, Kentrogonida, is shown to be ancestral and most likely a homologue of the juvenile stage of a conventional thoracican barnacle. The mode of host inoculation found in the suborder Akentrogonida, where the last pelagic larval stage directly injects the parasitic material into the heamolymph of the host is derived, and has evolved only once within the Rhizocephala. Lastly, our results show that the ancestral host for extant rhizocephalans appears to be the anomuran crustaceans (Anomura), which includes hermit crabs and squat lobsters.

  3. The Multipartite Mitochondrial Genome of Liposcelis bostrychophila: Insights into the Evolution of Mitochondrial Genomes in Bilateral Animals

    PubMed Central

    Yuan, Ming-Long; Dou, Wei; Barker, Stephen C.; Wang, Jin-Jun

    2012-01-01

    Booklice (order Psocoptera) in the genus Liposcelis are major pests to stored grains worldwide and are closely related to parasitic lice (order Phthiraptera). We sequenced the mitochondrial (mt) genome of Liposcelis bostrychophila and found that the typical single mt chromosome of bilateral animals has fragmented into and been replaced by two medium-sized chromosomes in this booklouse; each of these chromosomes has about half of the genes of the typical mt chromosome of bilateral animals. These mt chromosomes are 8,530 bp (mt chromosome I) and 7,933 bp (mt chromosome II) in size. Intriguingly, mt chromosome I is twice as abundant as chromosome II. It appears that the selection pressure for compact mt genomes in bilateral animals favors small mt chromosomes when small mt chromosomes co-exist with the typical large mt chromosomes. Thus, small mt chromosomes may have selective advantages over large mt chromosomes in bilateral animals. Phylogenetic analyses of mt genome sequences of Psocodea (i.e. Psocoptera plus Phthiraptera) indicate that: 1) the order Psocoptera (booklice and barklice) is paraphyletic; and 2) the order Phthiraptera (the parasitic lice) is monophyletic. Within parasitic lice, however, the suborder Ischnocera is paraphyletic; this differs from the traditional view that each suborder of parasitic lice is monophyletic. PMID:22479490

  4. Monophyly of terrestrial adephagan beetles as indicated by three nuclear genes (Coleoptera: Carabidae and Trachypachidae)

    PubMed Central

    Maddison, D. R.; Moore, W.; Baker, M. D.; Ellis, T.M.; Ober, K.A.; Cannone, J.J.; Gutell, R.R.

    2009-01-01

    The beetle suborder Adephaga is traditionally divided into two sections on the basis of habitat, terrestrial Geadephaga and aquatic Hydradephaga. Monophyly of both groups is uncertain, and the relationship of the two groups has implications for inferring habitat transitions within Adephaga. Here we examine phylogenetic relationships of these groups using evidence provided by DNA sequences from all four suborders of beetles, including 60 species of Adephaga, four Archostemata, three Myxophaga, and ten Polyphaga. We studied 18S ribosomal DNA and 28S ribosomal DNA, aligned with consideration of secondary structure, as well as the nuclear protein-coding gene wingless. Independent and combined Bayesian, likelihood, and parsimony analyses of all three genes supported placement of Trachypachidae in a monophyletic Geadephaga, although for analyses of 28S rDNA and some parsimony analyses only if Coleoptera is constrained to be monophyletic. Most analyses showed limited support for the monophyly of Hydradephaga. Outside of Adephaga, there is support from the ribosomal genes for a sister group relationship between Adephaga and Polyphaga. Within the small number of sampled Polyphaga, analyses of 18S rDNA, wingless, and the combined matrix supports monophyly of Polyphaga exclusive of Scirtoidea. Unconstrained analyses of the evolution of habitat suggest that Adephaga was ancestrally aquatic with one transition to terrestrial. However, in analyses constrained to disallow changes from aquatic to terrestrial habitat, the phylogenies imply two origins of aquatic habit within Adephaga. PMID:19789725

  5. Sexual selection, sexual size dimorphism and Rensch's rule in Odonata.

    PubMed

    Serrano-Meneses, M A; Córdoba-Aguilar, A; Azpilicueta-Amorín, M; González-Soriano, E; Székely, T

    2008-09-01

    Odonata (dragonflies and damselflies) exhibit a range of sexual size dimorphism (SSD) that includes species with male-biased (males > females) or female-biased SSD (males < females) and species exhibiting nonterritorial or territorial mating strategies. Here, we use phylogenetic comparative analyses to investigate the influence of sexual selection on SSD in both suborders: dragonflies (Anisoptera) and damselflies (Zygoptera). First, we show that damselflies have male-biased SSD, and exhibit an allometric relationship between body size and SSD, that is consistent with Rensch's rule. Second, SSD of dragonflies is not different from unit, and this suborder does not exhibit Rensch's rule. Third, we test the influence of sexual selection on SSD using proxy variables of territorial mating strategy and male agility. Using generalized least squares to account for phylogenetic relationships between species, we show that male-biased SSD increases with territoriality in damselflies, but not in dragonflies. Finally, we show that nonagile territorial odonates exhibit male-biased SSD, whereas male agility is not related to SSD in nonterritorial odonates. These results suggest that sexual selection acting on male sizes influences SSD in Odonata. Taken together, our results, along with avian studies (bustards and shorebirds), suggest that male agility influences SSD, although this influence is modulated by territorial mating strategy and thus the likely advantage of being large. Other evolutionary processes, such as fecundity selection and viability selection, however, need further investigation.

  6. Higher classification and phylogeny of Euglenozoa.

    PubMed

    Cavalier-Smith, Thomas

    2016-10-01

    Discoveries of numerous new taxa and advances in ultrastructure and sequence phylogeny (including here the first site-heterogeneous 18S rDNA trees) require major improvements to euglenozoan higher-level taxonomy. I therefore divide Euglenozoa into three subphyla of substantially different body plans: Euglenoida with pellicular strips; anaerobic Postgaardia (class Postgaardea) dependent on surface bacteria and with uniquely modified feeding apparatuses; and new subphylum Glycomonada characterised by glycosomes (Kinetoplastea, Diplonemea). Euglenoida comprise two new infraphyla: Entosiphona with three feeding rods and Dipilida ancestrally with two. Dipilida comprise basal superclass Rigimonada with longitudinal rigid strips [i.e. new classes Stavomonadea (Petalomonadida, Decastavida and new order Heterostavida) and Ploeotarea (Ploeotiida) with contrasting oral cytoskeletons] and derived superclass Spirocuta with more numerous spirally arranged, often slideable, strips (clade Peranemea/Euglenophyceae) and a different, highly conserved microtubule pattern at strip joints. Peranemea comprise four orders: Peranemida (anterior gliding, protrusible rods), and three new, Anisonemida (posterior gliders), Natomonadida (swimmers including phagotrophic new suborder Metanemina and osmotrophic suborder Rhabdomonadina), and Acroglissida (anterior gliders with cytoproct). I establish orders Entosiphonida, Rapazida, Bihospitida; and seven new euglenoid families (Entosiphonidae, peranemean Neometanemidae, Rapazidae, two stavomonad, two ploeotiid) and three new postgaardian, and three kinetoplastid families (Neobodonidae, Rhynchomonadidae, Parabodonidae), plus new diplonemid family Hemistasiidae for Hemistasia.

  7. Systematics of stalked jellyfishes (Cnidaria: Staurozoa)

    PubMed Central

    Hirano, Yayoi M.; Mills, Claudia E.; Falconer, Audrey; Fenwick, David

    2016-01-01

    Staurozoan classification is highly subjective, based on phylogeny-free inferences, and suborders, families, and genera are commonly defined by homoplasies. Additionally, many characters used in the taxonomy of the group have ontogenetic and intraspecific variation, and demand new and consistent assessments to establish their correct homologies. Consequently, Staurozoa is in need of a thorough systematic revision. The aim of this study is to propose a comprehensive phylogenetic hypothesis for Staurozoa, providing the first phylogenetic classification for the group. According to our working hypothesis based on a combined set of molecular data (mitochondrial markers COI and 16S, and nuclear markers ITS, 18S, and 28S), the traditional suborders Cleistocarpida (animals with claustrum) and Eleutherocarpida (animals without claustrum) are not monophyletic. Instead, our results show that staurozoans are divided into two groups, herein named Amyostaurida and Myostaurida, which can be distinguished by the absence/presence of interradial longitudinal muscles in the peduncle, respectively. We propose a taxonomic revision at the family and genus levels that preserves the monophyly of taxa. We provide a key for staurozoan genera and discuss the evolution of the main characters used in staurozoan taxonomy. PMID:27168970

  8. Modifications of the falciform process in the eye of beloniformes (Teleostei: Atherinomorpha): evolution of a curtain-like septum in the eye.

    PubMed

    Reckel, Frank; Melzer, Roland R

    2004-04-01

    In order to comparatively analyze curtain-like septa in the eyes of visually orientated "close-to-surface-predators" among atherinomorph teleosts, we examined the eyes of 24 atherinomorph species under a binocular microscope with regard to the falciform process and related structures in the vitreous cavity. Additionally, falciform process samples were analyzed by transmission electron microscopy. All the studied representatives of the Cyprinodontiformes and Atheriniformes, and of one of the beloniform suborder, Adrianichthyioidei, possess a "typical" processus falciformis. In the eyes of the representatives of the other beloniform suborder, Belonoidei, however, pigmented structures that originate in the region of the optic disc and protrude into the vitreous cavity were noted. In the Hemiramphidae (halfbeaks) and Exocoetidae (flying fishes) these pigmented structures have a more cone-like shape, whereas in the Belonidae (needlefishes) and Scomberesocidae (sauries) horizontally oriented heavily pigmented curtain-like septa occur that divide the vitreous cavity dorsoventrally. It is suggested that the "typical" processus falciformis represents a plesiomorphic feature within the Atherinomorpha, whereas the pigmented modifications of the falciform process must be seen as a synapomorphic character state of the Belonoidei. The curtain-like septum of the Belonidae and Scomberesocidae might have evolved from the cone-like structures that are found in the Exocoetoidea. The functional significance of the pigmented structures in the eye is as yet not clear, except for the curtain-like septum found in Belonidae. It might play a role in visual orientation near the water surface at Snell's window.

  9. Characterization of the complete mitogenomes of two Neoscona spiders (Araneae: Araneidae) and its phylogenetic implications.

    PubMed

    Wang, Zheng-Liang; Li, Chao; Fang, Wen-Yuan; Yu, Xiao-Ping

    2016-09-30

    The complete mitogenomes of two orb-weaving spiders Neoscona doenitzi and Neoscona nautica were determined and a comparative mitogenomic analysis was performed to depict evolutionary trends of spider mitogenomes. The circular mitogenomes are 14,161bp with A+T content of 74.6% in N. doenitzi and 14,049bp with A+T content of 78.8% in N. nautica, respectively. Both mitogenomes contain a standard set of 37 genes typically presented in metazoans. Gene content and orientation are identical to all previously sequenced spider mitogenomes, while gene order is rearranged by tRNAs translocation when compared with the putative ancestral gene arrangement pattern presented by Limulus polyphemus. A comparative mitogenomic analysis reveals that the nucleotide composition bias is obviously divergent between spiders in suborder Opisthothelae and Mesothelae. The loss of D-arm in the trnS(UCN) among all of Opisthothelae spiders highly suggested that this common feature is a synapomorphy for entire suborder Opisthothelae. Moreover, the trnS(AGN) in araneoids preferred to use TCT as an anticodon rather than the typical anticodon GCT. Phylogenetic analysis based on the 13 protein-coding gene sequences consistently yields trees that nest the two Neoscona spiders within Araneidae and recover superfamily Araneoidea as a monophyletic group. The molecular information acquired from the results of this study should be very useful for future research on mitogenomic evolution and genetic diversities in spiders.

  10. Independent evolution of the specialized pharyngeal jaw apparatus in cichlid and labrid fishes

    PubMed Central

    Mabuchi, Kohji; Miya, Masaki; Azuma, Yoichiro; Nishida, Mutsumi

    2007-01-01

    Background Fishes in the families Cichlidae and Labridae provide good probable examples of vertebrate adaptive radiations. Their spectacular trophic radiations have been widely assumed to be due to structural key innovation in pharyngeal jaw apparatus (PJA), but this idea has never been tested based on a reliable phylogeny. For the first step of evaluating the hypothesis, we investigated the phylogenetic positions of the components of the suborder Labroidei (including Pomacentridae and Embiotocidae in addition to Cichlidae and Labridae) within the Percomorpha, the most diversified (> 15,000 spp) crown clade of teleosts. We examined those based on 78 whole mitochondrial genome sequences (including 12 newly determined sequences) through partitioned Bayesian analyses with concatenated sequences (13,933 bp). Results The resultant phylogenies indicated that the Labridae and the remaining three labroid families have diverged basally within the Percomorpha, and monophyly of the suborder was confidently rejected by statistical tests using Bayes factors. Conclusion The resultant phylogenies indicated that the specified PJA evolved independently at least twice, once in Labridae and once in the common ancestor of the remaining three labroid families (including the Cichlidae). Because the independent evolution of pharyngeal jaws appears to have been followed by trophic radiations, we consider that our result supports, from the aspect of historical repeatability, the idea that the evolution of the specialized PJA provided these lineages with the morphological potential for their spectacular trophic radiations. The present result will provide a new framework for the study of functional morphology and genetic basis of their PJA. PMID:17263894

  11. Resilin in dragonfly and damselfly wings and its implications for wing flexibility.

    PubMed

    Donoughe, Seth; Crall, James D; Merz, Rachel A; Combes, Stacey A

    2011-12-01

    Although there is mounting evidence that passive mechanical dynamics of insect wings play an integral role in insect flight, our understanding of the structural details underlying insect wing flexibility remains incomplete. Here, we use comparative morphological and mechanical techniques to illuminate the function and diversity of two mechanisms within Odonata wings presumed to affect dynamic wing deformations: flexible resilin vein-joints and cuticular spikes. Mechanical tests show that joints with more resilin have lower rotational stiffness and deform more in response to a load applied to an intact wing. Morphological studies of 12 species of Odonata reveal that resilin joints and cuticular spikes are widespread taxonomically, yet both traits display a striking degree of morphological and functional diversity that follows taxonomically distinct patterns. Interestingly, damselfly wings (suborder Zygoptera) are mainly characterized by vein-joints that are double-sided (containing resilin both dorsally and ventrally), whereas dragonfly wings (suborder Epiprocta) are largely characterized by single-sided vein-joints (containing resilin either ventrally or dorsally, but not both). The functional significance and diversity of resilin joints and cuticular spikes could yield insight into the evolutionary relationship between form and function of wings, as well as revealing basic principles of insect wing mechanical design.

  12. Embryonic development of Ampheres leucopheus and Iporangaia pustulosa (Arachnida: Opiliones: Gonyleptidae).

    PubMed

    Gnaspini, Pedro; Lerche, Cristiano Frederico

    2010-09-15

    The first studies concerning the embryonic development of harvestmen started in the late 19th century, and focused mostly on holarctic species, and only three species of the suborder Laniatores (the largest, among the four suborders considered presently) were studied. Moreover, the last studies on embryology of harvestmen were made during the late 1970s. This study focused on the embryonic development of Ampheres leucopheus (Gonyleptidae, Caelopyginae) and Iporangaia pustulosa (Gonyleptidae, Progonyleptoidellinae). The embryonic development was followed in the field, by taking daily photographs of different eggs during about 2 months. When laid, eggs of A. leucopheus and I. pustulosa have approximately 1.13 and 1.30 mm in diameter, respectively, and the second is embedded in a large amount of mucus. The eggs grow, mainly due to water absorption at the beginning of the process, and they reach a diameter of about 1.35 and 1.59 mm, respectively, close to hatching. It took, respectively, 29-56 days and 35-66 days from egg laying to hatching. For the description of the embryonic development, we use photographs from the field, SEM micrographs, and histological analysis. This allowed us, for instance, to document the progression of structures and pigmentation directly from live embryos in the field, and to record microstructures, such as the presence of perforations in the cuticle of the embryo in the place where eyes are developing. Yet, contrary to what was expected in the literature, we record an egg tooth in one of the studied laniatoreans.

  13. High-level phylogeny of the Coleoptera inferred with mitochondrial genome sequences.

    PubMed

    Yuan, Ming-Long; Zhang, Qi-Lin; Zhang, Li; Guo, Zhong-Long; Liu, Yong-Jian; Shen, Yu-Ying; Shao, Renfu

    2016-11-01

    The Coleoptera (beetles) exhibits tremendous morphological, ecological, and behavioral diversity. To better understand the phylogenetics and evolution of beetles, we sequenced three complete mitogenomes from two families (Cleridae and Meloidae), which share conserved mitogenomic features with other completely sequenced beetles. We assessed the influence of six datasets and three inference methods on topology and nodal support within the Coleoptera. We found that both Bayesian inference and maximum likelihood with homogeneous-site models were greatly affected by nucleotide compositional heterogeneity, while the heterogeneous-site mixture model in PhyloBayes could provide better phylogenetic signals for the Coleoptera. The amino acid dataset generated more reliable tree topology at the higher taxonomic levels (i.e. suborders and series), where the inclusion of rRNA genes and the third positions of protein-coding genes improved phylogenetic inference at the superfamily level, especially under a heterogeneous-site model. We recovered the suborder relationships as (Archostemata+Adephaga)+(Myxophaga+Polyphaga). The series relationships within Polyphaga were recovered as (Scirtiformia+(Elateriformia+((Bostrichiformia+Scarabaeiformia+Staphyliniformia)+Cucujiformia))). All superfamilies within Cucujiformia were recovered as monophyletic. We obtained a cucujiform phylogeny of (Cleroidea+(Coccinelloidea+((Lymexyloidea+Tenebrionoidea)+(Cucujoidea+(Chrysomeloidea+Curculionoidea))))). This study showed that although tree topologies were sensitive to data types and inference methods, mitogenomic data could provide useful information for resolving the Coleoptera phylogeny at various taxonomic levels by using suitable datasets and heterogeneous-site models.

  14. Genomic Characterization of Yogue, Kasokero, Issyk-Kul, Keterah, Gossas, and Thiafora Viruses: Nairoviruses Naturally Infecting Bats, Shrews, and Ticks

    PubMed Central

    Walker, Peter J.; Widen, Steven G.; Firth, Cadhla; Blasdell, Kim R.; Wood, Thomas G.; Travassos da Rosa, Amelia P. A.; Guzman, Hilda; Tesh, Robert B.; Vasilakis, Nikos

    2015-01-01

    The genus Nairovirus of arthropod-borne bunyaviruses includes the important emerging human pathogen, Crimean–Congo hemorrhagic fever virus (CCHFV), as well as Nairobi sheep disease virus and many other poorly described viruses isolated from mammals, birds, and ticks. Here, we report genome sequence analysis of six nairoviruses: Thiafora virus (TFAV) that was isolated from a shrew in Senegal; Yogue (YOGV), Kasokero (KKOV), and Gossas (GOSV) viruses isolated from bats in Senegal and Uganda; Issyk-Kul virus (IKV) isolated from bats in Kyrgyzstan; and Keterah virus (KTRV) isolated from ticks infesting a bat in Malaysia. The S, M, and L genome segments of each virus were found to encode proteins corresponding to the nucleoprotein, polyglycoprotein, and polymerase protein of CCHFV. However, as observed in Leopards Hill virus (LPHV) and Erve virus (ERVV), polyglycoproteins encoded in the M segment lack sequences encoding the double-membrane-spanning CCHFV NSm protein. Amino acid sequence identities, complement-fixation tests, and phylogenetic analysis indicated that these viruses cluster into three groups comprising KKOV, YOGV, and LPHV from bats of the suborder Yingochiroptera; KTRV, IKV, and GOSV from bats of the suborder Yangochiroptera; and TFAV and ERVV from shrews (Soricomorpha: Soricidae). This reflects clade-specific host and vector associations that extend across the genus. PMID:26324724

  15. The evolutionary history of cetacean brain and body size.

    PubMed

    Montgomery, Stephen H; Geisler, Jonathan H; McGowen, Michael R; Fox, Charlotte; Marino, Lori; Gatesy, John

    2013-11-01

    Cetaceans rival primates in brain size relative to body size and include species with the largest brains and biggest bodies to have ever evolved. Cetaceans are remarkably diverse, varying in both phenotypes by several orders of magnitude, with notable differences between the two extant suborders, Mysticeti and Odontoceti. We analyzed the evolutionary history of brain and body mass, and relative brain size measured by the encephalization quotient (EQ), using a data set of extinct and extant taxa to capture temporal variation in the mode and direction of evolution. Our results suggest that cetacean brain and body mass evolved under strong directional trends to increase through time, but decreases in EQ were widespread. Mysticetes have significantly lower EQs than odontocetes due to a shift in brain:body allometry following the divergence of the suborders, caused by rapid increases in body mass in Mysticeti and a period of body mass reduction in Odontoceti. The pattern in Cetacea contrasts with that in primates, which experienced strong trends to increase brain mass and relative brain size, but not body mass. We discuss what these analyses reveal about the convergent evolution of large brains, and highlight that until recently the most encephalized mammals were odontocetes, not primates.

  16. The evolution of body size, antennal size and host use in parasitoid wasps (Hymenoptera: Chalcidoidea): a phylogenetic comparative analysis.

    PubMed

    Symonds, Matthew R E; Elgar, Mark A

    2013-01-01

    Chalcidoid wasps represent one of the most speciose superfamilies of animals known, with ca. 23,000 species described of which many are parasitoids. They are extremely diverse in body size, morphology and, among the parasitoids, insect hosts. Parasitic chalcidoids utilise a range of behavioural adaptations to facilitate exploitation of their diverse insect hosts, but how host use might influence the evolution of body size and morphology is not known in this group. We used a phylogenetic comparative analysis of 126 chalcidoid species to examine whether body size and antennal size showed evolutionary correlations with aspects of host use, including host breadth (specificity), host identity (orders of insects parasitized) and number of plant associates. Both morphological features and identity of exploited host orders show strong phylogenetic signal, but host breadth does not. Larger body size in these wasps was weakly associated with few plant genera, and with more specialised host use, and chalcidoid wasps that parasitize coleopteran hosts tend to be larger. Intriguingly, chalcidoid wasps that parasitize hemipteran hosts are both smaller in size in the case of those parasitizing the suborder Sternorrhyncha and have relatively larger antennae, particularly in those that parasitize other hemipteran suborders. These results suggest there are adaptations in chalcidoid wasps that are specifically associated with host detection and exploitation.

  17. Primary structure of pancreatic polypeptide from four species of Perissodactyla (Przewalski's horse, zebra, rhino, tapir).

    PubMed

    Henry, J S; Lance, V A; Conlon, J M

    1991-12-01

    Pancreatic polypeptide (PP) has been purified from extracts of the pancreas of four species of odd-toed ungulates (Perissodactyla): Przewalski's horse, mountain zebra, white rhinoceros, and mountain tapir. The amino acid sequence of Przewalski's horse pancreatic polypeptide was established as Ala-Pro-Met-Glu-Pro-Val-Tyr-Pro-Gly-Asp10-Asn- Ala-Thr-Pro-Glu-Gln-Met-Ala-Gln-Tyr20-Ala-Ala-Glu-Leu-Arg-Arg-Tyr- Ile-Asn-Met30 - Leu-Thr-Arg-Pro-Arg-Tyr.NH2. Zebra PP was identical to Przewalski's horse PP, rhinoceros PP contained three substitutions relative to the horse (Ser for Ala1, Leu for Met3, and Glu for Gln16), and tapir PP contained one substitution relative to the horse (Leu for Met3). On the basis of morphological characteristics and the fossil record, the rhinocerotids are classified with the tapirids in the suborder Ceratomorpha, whereas the horse and zebra belong to a separate suborder, Hippomorpha. On the basis of structural similarity of the PP molecules, however, it would appear that the tapir is more closely related to the horse than to the rhinoceros. These observations provide a further example of the need for extreme caution when inferring taxonomic or phylogenetic relationships between species from the structures of homologous peptides.

  18. Systematics of stalked jellyfishes (Cnidaria: Staurozoa).

    PubMed

    Miranda, Lucília S; Hirano, Yayoi M; Mills, Claudia E; Falconer, Audrey; Fenwick, David; Marques, Antonio C; Collins, Allen G

    2016-01-01

    Staurozoan classification is highly subjective, based on phylogeny-free inferences, and suborders, families, and genera are commonly defined by homoplasies. Additionally, many characters used in the taxonomy of the group have ontogenetic and intraspecific variation, and demand new and consistent assessments to establish their correct homologies. Consequently, Staurozoa is in need of a thorough systematic revision. The aim of this study is to propose a comprehensive phylogenetic hypothesis for Staurozoa, providing the first phylogenetic classification for the group. According to our working hypothesis based on a combined set of molecular data (mitochondrial markers COI and 16S, and nuclear markers ITS, 18S, and 28S), the traditional suborders Cleistocarpida (animals with claustrum) and Eleutherocarpida (animals without claustrum) are not monophyletic. Instead, our results show that staurozoans are divided into two groups, herein named Amyostaurida and Myostaurida, which can be distinguished by the absence/presence of interradial longitudinal muscles in the peduncle, respectively. We propose a taxonomic revision at the family and genus levels that preserves the monophyly of taxa. We provide a key for staurozoan genera and discuss the evolution of the main characters used in staurozoan taxonomy.

  19. The First Chameleon Transcriptome: Comparative Genomic Analysis of the OXPHOS System Reveals Loss of COX8 in Iguanian Lizards

    PubMed Central

    Bar-Yaacov, Dan; Bouskila, Amos; Mishmar, Dan

    2013-01-01

    Recently, we found dramatic mitochondrial DNA divergence of Israeli Chamaeleo chamaeleon populations into two geographically distinct groups. We aimed to examine whether the same pattern of divergence could be found in nuclear genes. However, no genomic resource is available for any chameleon species. Here we present the first chameleon transcriptome, obtained using deep sequencing (SOLiD). Our analysis identified 164,000 sequence contigs of which 19,000 yielded unique BlastX hits. To test the efficacy of our sequencing effort, we examined whether the chameleon and other available reptilian transcriptomes harbored complete sets of genes comprising known biochemical pathways, focusing on the nDNA-encoded oxidative phosphorylation (OXPHOS) genes as a model. As a reference for the screen, we used the human 86 (including isoforms) known structural nDNA-encoded OXPHOS subunits. Analysis of 34 publicly available vertebrate transcriptomes revealed orthologs for most human OXPHOS genes. However, OXPHOS subunit COX8 (Cytochrome C oxidase subunit 8), including all its known isoforms, was consistently absent in transcriptomes of iguanian lizards, implying loss of this subunit during the radiation of this suborder. The lack of COX8 in the suborder Iguania is intriguing, since it is important for cellular respiration and ATP production. Our sequencing effort added a new resource for comparative genomic studies, and shed new light on the evolutionary dynamics of the OXPHOS system. PMID:24009133

  20. Phylogenomic analyses of bat subordinal relationships based on transcriptome data

    PubMed Central

    Lei, Ming; Dong, Dong

    2016-01-01

    Bats, order Chiroptera, are one of the largest monophyletic clades in mammals. Based on morphology and behaviour bats were once differentiated into two suborders Megachiroptera and Microchiroptera Recently, researchers proposed alternative views of chiropteran classification (suborders Yinpterochiroptera and Yangochiroptera) based on morphological, molecular and fossil evidence. Since genome-scale data can significantly increase the number of informative characters for analysis, transcriptome RNA-seq data for 12 bat taxa were generated in an attempt to resolve bat subordinal relationships at the genome level. Phylogenetic reconstructions were conducted using up to 1470 orthologous genes and 634,288 aligned sites. We found strong support for the Yinpterochiroptera-Yangochiroptera classification. Next, we built expression distance matrices for each species and reconstructed gene expression trees. The tree is highly consistent with sequence-based phylogeny. We also examined the influence of taxa sampling on the performance of phylogenetic methods, and found that the topology is robust to sampling. Relaxed molecular clock estimates the divergence between Yinpterochiroptera and Yangochiroptera around 63 million years ago. The most recent common ancestor of Yinpterochiroptera, corresponding to the split between Rhinolophoidea and Pteropodidae (Old World Fruit bats), is estimated to have occurred 60 million years ago. Our work provided a valuable resource to further explore the evolutionary relationship within bats. PMID:27291671

  1. A new genus and species for the first recorded cave-dwelling Cavernicola (Platyhelminthes) from South America

    PubMed Central

    Leal-Zanchet, Ana Maria; de Souza, Stella Teles; Ferreira, Rodrigo Lopes

    2014-01-01

    Abstract Species diversity of Brazilian cave fauna has been seriously underestimated. A karst area located in Felipe Guerra, northeastern Brazil, which is a hotspot of subterranean diversity in Brazil, has revealed more than 20 troglobitic species, most of them still undescribed. Based on recent samplings in this karst area, we document the occurrence of the suborder Cavernicola (Platyhelminthes) in South American hypogean environments for the first time and describe a new genus and species for this suborder. Hausera Leal-Zanchet & Souza, gen. n. has features concordant with those defined for the family Dimarcusidae. The new genus is characterized by two unique features, viz. an intestine extending dorsally to the brain and ovovitelline ducts located dorsally to the nerve cords, which is complemented by a combination of other characters. The type-specimens of Hausera hauseri Leal-Zanchet & Souza, sp. n. are typical stygobionts, unpigmented and eyeless, and they may constitute an oceanic relict as is the case of other stygobiotic invertebrates found in this karst area in northeastern Brazil. PMID:25349486

  2. Extensive mitochondrial gene arrangements in coleoid Cephalopoda and their phylogenetic implications.

    PubMed

    Akasaki, Tetsuya; Nikaido, Masato; Tsuchiya, Kotaro; Segawa, Susumu; Hasegawa, Masami; Okada, Norihiro

    2006-03-01

    We determined the complete mitochondrial genomes of five cephalopods of the Subclass Coleoidea (Suborder Oegopsida: Watasenia scintillans, Todarodes pacificus, Suborder Myopsida: Sepioteuthis lessoniana, Order Sepiida: Sepia officinalis, and Order Octopoda: Octopus ocellatus) and used them to infer phylogenetic relationships. In our Maximum Likelihood (ML) tree, sepiids (cuttlefish) are at the most basal position of all decapodiformes, and oegopsids and myopsids form a monophyletic clade, thus supporting the traditional classification of the Order Teuthida. We detected extensive gene rearrangements in the mitochondrial genomes of broad cephalopod groups. It is likely that the arrangements of mitochondrial genes in Oegopsida and Sepiida were derived from those of Octopoda, which is thought to be the ancestral order, by entire gene duplication and random gene loss. Oegopsida in particular has undergone long-range gene duplications. We also found that the mitochondrial gene arrangement of Sepioteuthis lessoniana differs from that of Loligo bleekeri, although they belong to the same family. Analysis of both the phylogenetic tree and mitochondrial gene rearrangements of coleoid Cephalopoda suggests that each mitochondrial gene arrangement was acquired after the divergence of each lineage.

  3. Intraclass Evolution and Classification of the Colpodea (Ciliophora)

    PubMed Central

    FOISSNER, WILHELM; STOECK, THORSTEN; AGATHA, SABINE; DUNTHORN, MICAH

    2012-01-01

    Using nine new taxa and statistical inferences based on morphological and molecular data, we analyze the evolution within the class Colpodea. The molecular and cladistic analyses show four well-supported clades: platyophryids, bursariomorphids, cyrtolophosidids, and colpodids. There is a widespread occurrence of homoplasies, affecting even conspicuous morphological characteristics, e.g. the inclusion of the micronucleus in the perinuclear space of the macronucleus. The most distinct changes in the morphological classification are the lack of a basal divergence into two subclasses and the split of the cyrtolophosidids into two main clades, differing mainly by the presence vs. absence of an oral cavity. The most complex clade is that of the colpodids. We partially reconcile the morphological and molecular data using evolutionary systematics, providing a scenario in which the colpodids evolved from a Bardeliella-like ancestor and the genus Colpoda performed an intense adaptive radiation, giving rise to three main clades: Colpodina n. subord., Grossglockneriina, and Bryophryina. Three new taxa are established: Colpodina n. subord., Tillinidae n. fam., and Ottowphryidae n. fam. Colpodean evolution and classification are far from being understood because sequences are lacking for most species and half of their diversity is possibly undescribed. PMID:21762424

  4. The Evolution of Body Size, Antennal Size and Host Use in Parasitoid Wasps (Hymenoptera: Chalcidoidea): A Phylogenetic Comparative Analysis

    PubMed Central

    Symonds, Matthew R. E.; Elgar, Mark A.

    2013-01-01

    Chalcidoid wasps represent one of the most speciose superfamilies of animals known, with ca. 23,000 species described of which many are parasitoids. They are extremely diverse in body size, morphology and, among the parasitoids, insect hosts. Parasitic chalcidoids utilise a range of behavioural adaptations to facilitate exploitation of their diverse insect hosts, but how host use might influence the evolution of body size and morphology is not known in this group. We used a phylogenetic comparative analysis of 126 chalcidoid species to examine whether body size and antennal size showed evolutionary correlations with aspects of host use, including host breadth (specificity), host identity (orders of insects parasitized) and number of plant associates. Both morphological features and identity of exploited host orders show strong phylogenetic signal, but host breadth does not. Larger body size in these wasps was weakly associated with few plant genera, and with more specialised host use, and chalcidoid wasps that parasitize coleopteran hosts tend to be larger. Intriguingly, chalcidoid wasps that parasitize hemipteran hosts are both smaller in size in the case of those parasitizing the suborder Sternorrhyncha and have relatively larger antennae, particularly in those that parasitize other hemipteran suborders. These results suggest there are adaptations in chalcidoid wasps that are specifically associated with host detection and exploitation. PMID:24205189

  5. Thysanoptera of Bulgaria

    PubMed Central

    Karadjova, Olia; Krumov, Vladimir

    2015-01-01

    Abstract The present checklist includes data on the species composition, geographic distribution and feeding preferences of thrips species in Bulgaria. In total, 155 species in 48 genera are listed. Of these, 125 species belong to suborder Terebrantia and include 103 species of 33 genera in family Thripidae, 14 species of two genera in Aeolothripidae, seven species of two genera in Melanthripidae and one species in Fauriellidae. In suborder Tubulifera, 30 species of 10 genera in the single family Phlaeothripidae are listed. Of the 155 Bulgarian thrips species, 87.7% are phytophagous, 4.5% are obligate predators, 5.8% are mycophagous and 1.9% are with unknown feeding preferences. Fourteen pest species are listed for Bulgaria, of which Frankliniella occidentalis, Thrips tabaci and Haplothrips tritici are of economic importance. The list provides detailed information on the horizontal and vertical distribution of Thysanoptera in 5 regions and 45 subregions of Bulgaria. The present paper also includes an evaluation of the biodiversity of Thysanoptera and the extent to which each region of the country has been studied. PMID:26019678

  6. First evidence for (TTAGG)n telomeric sequence and sex chromosome post-reduction in Coleorrhyncha (Insecta, Hemiptera)

    PubMed Central

    Kuznetsova, Valentina G.; Grozeva, Snejana M.; Hartung, Viktor; Anokhin, Boris A.

    2015-01-01

    Abstract Telomeric repeats are general and significant structures of eukaryotic chromosomes. However, nothing is known about the molecular structure of telomeres in the enigmatic hemipteran suborder Coleorrhyncha (moss bugs) commonly considered as the sister group to the suborder Heteroptera (true bugs). The true bugs are known to differ from the rest of the Hemiptera in that they display an inverted sequence of sex chromosome divisions in male meiosis, the so-called sex chromosome post-reduction. To date, there has been no information about meiosis in Coleorrhyncha. Here we report a cytogenetic observation of Peloridium pomponorum, a representative of the single extant coleorrhynchan family Peloridiidae, using the standard chromosome staining and fluorescence in situ hybridization (FISH) with a (TTAGG)n telomeric probe. We show that Peloridium pomponorum displays 2n = 31 (30A + X) in males, the classical insect (TTAGG)n telomere organization and sex chromosome post-reduction during spermatocyte meiosis. The plesiomorphic insect-type (TTAGG)n telomeric sequence is suggested to be preserved in Coleorrhyncha and in a basal heteropteran infraorder Nepomorpha, but absent (lost) in the advanced heteropteran lineages Cimicomorpha and Pentatomomorpha. The telomere structure in other true bug infraorders is currently unknown. We consider here the inverted sequence of sex chromosome divisions as a synapomorphy of the group Coleorrhyncha + Heteroptera. PMID:26753072

  7. Genomic Characterization of Yogue, Kasokero, Issyk-Kul, Keterah, Gossas, and Thiafora Viruses: Nairoviruses Naturally Infecting Bats, Shrews, and Ticks.

    PubMed

    Walker, Peter J; Widen, Steven G; Firth, Cadhla; Blasdell, Kim R; Wood, Thomas G; Travassos da Rosa, Amelia P A; Guzman, Hilda; Tesh, Robert B; Vasilakis, Nikos

    2015-11-01

    The genus Nairovirus of arthropod-borne bunyaviruses includes the important emerging human pathogen, Crimean-Congo hemorrhagic fever virus (CCHFV), as well as Nairobi sheep disease virus and many other poorly described viruses isolated from mammals, birds, and ticks. Here, we report genome sequence analysis of six nairoviruses: Thiafora virus (TFAV) that was isolated from a shrew in Senegal; Yogue (YOGV), Kasokero (KKOV), and Gossas (GOSV) viruses isolated from bats in Senegal and Uganda; Issyk-Kul virus (IKV) isolated from bats in Kyrgyzstan; and Keterah virus (KTRV) isolated from ticks infesting a bat in Malaysia. The S, M, and L genome segments of each virus were found to encode proteins corresponding to the nucleoprotein, polyglycoprotein, and polymerase protein of CCHFV. However, as observed in Leopards Hill virus (LPHV) and Erve virus (ERVV), polyglycoproteins encoded in the M segment lack sequences encoding the double-membrane-spanning CCHFV NSm protein. Amino acid sequence identities, complement-fixation tests, and phylogenetic analysis indicated that these viruses cluster into three groups comprising KKOV, YOGV, and LPHV from bats of the suborder Yingochiroptera; KTRV, IKV, and GOSV from bats of the suborder Yangochiroptera; and TFAV and ERVV from shrews (Soricomorpha: Soricidae). This reflects clade-specific host and vector associations that extend across the genus.

  8. A Comparative Analysis of Feeding and Trophic Level Ecology in Stingrays (Rajiformes; Myliobatoidei) and Electric Rays (Rajiformes: Torpedinoidei)

    PubMed Central

    Jacobsen, Ian P.; Bennett, Mike B.

    2013-01-01

    Standardised diets and trophic level (TL) estimates were calculated for 75 ray species from the suborders Myliobatoidei (67 spp.) and Torpedinoidei (8 spp.). Decapod crustaceans (31.71±3.92%) and teleost fishes (16.45±3.43%) made the largest contribution to the standardised diet of the Myliobatoidei. Teleost fishes (37.40±16.09%) and polychaete worms (31.96±14.22%) were the most prominent prey categories in the standardised diet of the suborder Torpedinoidei. Cluster analysis identified nine major trophic guilds the largest of which were decapod crustaceans (24 species), teleost fishes (11 species) and molluscs (11 species). Trophic level estimates for rays ranged from 3.10 for Potamotrygon falkneri to 4.24 for Gymnura australis, Torpedo marmorata and T. nobiliana. Secondary consumers with a TL <4.00 represented 84% of the species examined, with the remaining 12 species (16%) classified as tertiary consumers (TL ≥4.00). Tertiary consumers included electric rays (Torpedo, 3 spp. and Hypnos, 1 sp.), butterfly rays (Gymnura, 4 spp.), stingrays (2 spp.) and Potamotrygonid stingrays (2 spp.). Feeding strategies were identified as the primary factor of influence with respect to Myliobatoidei and Torpedinoidei TL estimates with inter-family comparisons providing the greatest insight into Myliobatoidei and Torpedinoidei relationships. PMID:23936503

  9. Species delineation in Pampus (Perciformes) and the phylogenetic status of the Stromateoidei based on mitogenomics.

    PubMed

    Cui, Zhaoxia; Liu, Yuan; Li, Chi Pang; Chu, Ka Hou

    2011-02-01

    Recent studies on the mitochondrial genome have suggested that the duplications of tRNA and tandem repeats in the control region are important changes that are related to species diversity. This paper reports the study of mitogenomes from five Pampus (Perciformes, Stromateidae) species with very similar morphology. A duplicated tRNA(Met) gene in the tRNA-IQM region is present in Pampus sp. and P. punctatissimus. In the conserved sequence blocks of the control region, a duplicated CSB3 and promoter are found in Pampus sp. but are absent in P. minor. Moreover, a duplicated TAS is found in P. punctatissimus and P. chinensis. Based on the complete mitogenome sequence of Pampus sp., the first sequence reported from Stromateidae and the longest (17,694 bp) among the Perciformes mitogenomes, we conducted phylogenetic analysis to show that Stromateoidei and Scombroidei are more closely related to each other than to other Perciformes suborders. However, we reject the reciprocal monophyly of these two suborders.

  10. Characteristic variations in reflectance of surface soils

    NASA Technical Reports Server (NTRS)

    Stoner, E. R.; Baumgardner, M. F. (Principal Investigator)

    1982-01-01

    Surface soil samples from a wide range of naturally occurring soils were obtained for the purpose of studying the characteristic variations in soil reflectance as these variations relate to other soil properties and soil classification. A total 485 soil samples from the U.S. and Brazil representing 30 suborders of the 10 orders of 'Soil Taxonomy' was examined. The spectral bidirectional reflectance factor was measured on uniformly moist soils over the 0.52 to 2.32 micron wavelength range with a spectroradiometer adapted for indoor use. Five distinct soil spectral reflectance curve forms were identified according to curve shape, the presence or absence of absorption bands, and the predominance of soil organic matter and iron oxide composition. These curve forms were further characterized according to generically homogeneous soil properties in a manner similar to the subdivisions at the suborder level of 'Soil Taxonomy'. Results indicate that spectroradiometric measurements of soil spectral bidirectional reflectance factor can be used to characterize soil reflectance in terms that are meaningful to soil classification, genesis, and survey.

  11. Tuberculate ectomycorrhizae of angiosperms: The interaction between Boletus rubropunctus (Boletaceae) and Quercus species (Fagaceae) in the United States and Mexico.

    PubMed

    Smith, Matthew E; Pfister, Donald H

    2009-09-01

    Tuberculate ectomycorrhizae (TECM) are unique structures in which aggregates of ectomycorrhizal roots are encased in a covering of fungal hyphae. The function of TECM is unknown, but they probably enhance the nitrogen nutrition and disease resistance of host plants. Trees in the Pinaceae form TECM with species of Rhizopogon and Suillus (Suillineae, Boletales). Similar tubercules are found with diverse angiosperms, but their mycobionts have not been phylogenetically characterized. We collected TECM in Mexico and the USA that were similar to TECM in previous reports. We describe these TECM and identify both the plant and fungal symbionts. Plant DNA confirms that TECM hosts are Quercus species. ITS sequences from tubercules and sclerotia (hyphal aggregations that serve as survival structures) matched sporocarps of Boletus rubropunctus. Phylogenetic analyses confirm that this fungus belongs to the suborder Boletineae (Boletales). This is the first published report of TECM formation in the Boletineae and of sclerotia formation by a Boletus species. Our data suggest that the TECM morphology is an adaptive feature that has evolved separately in two suborders of Boletales (Suillineae and Boletineae) and that TECM formation is controlled by the mycobiont because TECM are found on distantly related angiosperm and gymnosperm host plants.

  12. Occurrence of plant parasitic nematodes (Tylenchina) in sugar beet fields in Fars province, Iran.

    PubMed

    Ebrahimi, N; Kheiri, A; Pakniat, M

    2004-01-01

    On a survey of plant parasitic nematode fauna, belonging to the suborder Tylenchina, about 110 soil and root samples were collected from different sugar beet field in fars Province in Iran. The samples were washed and the nematodes were extracted by Centrifugal Flotation Technique according to the modified method by De Grisse, 1969. They were fixed and transferred to glycerine, then permanent slides were mounted. Morphological and morphometrical characters of collected species were carefully studied and the characters were compared with the original descriptions and differences were discussed. In this study 18 species belonging to 11 different genera of subordes Tylenchina were identified as follows. Boleodorus thylactus, Ditylenchus destructor, D. dipsaci Geocenamus brevidens, G. rugosus, Helicotylenchus digonicus, H. pseudorobustus, H. vulgaris, Heterodera filipjevi, H. schachtii, Pratylenchus neglectus, P. thornei, Psilenchus hilarulus, P. hilarus, Stictylus mucronatus, Tylenchorhynchus ventrosinatus, Tylenchus davainei and Zygotylenchus guevarai. The species of the genera Ditylenchus, Heterodera, Pratylenchus and Psilenchus were comparatively more distributed than the others. This investigation revealed that sugar beet cyst nematode (Heterodera schachti) was found already in most sugar beet fields in this Province. Fathabod, Marvdasht and Tasuj-kwar were the most infested areas. Cysts collected from 100 gr. Of soil samples were 120 to 121 in number and the eggs and second stage larvae in each gr. of soil were 104.1 to 104.5 respectively.

  13. Feliform carnivores have a distinguished constitutive innate immune response.

    PubMed

    Heinrich, Sonja K; Wachter, Bettina; Aschenborn, Ortwin H K; Thalwitzer, Susanne; Melzheimer, Jörg; Hofer, Heribert; Czirják, Gábor Á

    2016-05-15

    Determining the immunological phenotype of endangered and threatened populations is important to identify those vulnerable to novel pathogens. Among mammals, members of the order Carnivora are particularly threatened by diseases. We therefore examined the constitutive innate immune system, the first line of protection against invading microbes, of six free-ranging carnivore species; the black-backed jackal (Canis mesomelas), the brown hyena (Hyena brunnea), the caracal (Caracal caracal), the cheetah (Acinonyx jubatus), the leopard (Panthera pardus) and the lion (Panthera leo) using a bacterial killing assay. The differences in immune responses amongst the six species were independent of their foraging behaviour, body mass or social organisation but reflected their phylogenetic relatedness. The bacterial killing capacity of black-backed jackals, a member of the suborder Caniformia, followed the pattern established for a wide variety of vertebrates. In contrast, the five representatives of the suborder Feliformia demonstrated a killing capacity at least an order of magnitude higher than any species reported previously, with a particularly high capacity in caracals and cheetahs. Our results suggest that the immunocompetence of threatened felids such as the cheetah has been underestimated and its assessment ought to consider both innate and adaptive components of the immune system.

  14. Complete mitochondrial genomes of two cockroaches, Blattella germanica and Periplaneta americana, and the phylogenetic position of termites.

    PubMed

    Xiao, Bo; Chen, Ai-Hui; Zhang, Yan-Yan; Jiang, Guo-Fang; Hu, Chao-Chao; Zhu, Chao-Dong

    2012-04-01

    The mitochondrial genomes are one of the most information-rich markers in phylogenetics. The relationships within superorder Dictyoptera have been debated in the literature. However, the closely related termites (Isoptera) are retained as unranked taxon within the order Blattaria (cockroaches). In this work, we sequenced the complete mitogenomes of two cockroaches, reconstructed the molecular phylogeny and attempted to infer the phylogenetic position of termites in Blattaria more reliably. The complete mtDNA nucleotide sequences of the peridomestic American cockroach (Periplaneta americana L.) and the domestic German cockroach (Blattella germanica L.) are 15,025 and 15,584 bp in size, respectively. The genome shares the gene order and orientation with previously known Blattaria mitogenomes. Most tRNAs could be folded into the typical cloverleaf secondary structure, but the tRNA-Ser (AGN) of P. americana appears to be missing the dihydrouridine arm. Using nucleotide and amino acid sequences as phylogenetic markers, we proposed that termites should be treated as a superfamily (Termitoidea) of cockroaches. We suggested that Polyphagoidea was the sister group of Termitoidea in Blattaria and supported that the suborder Caelifera is more closely related to the Phasmatodea than to the suborder Ensifera of Orthoptera.

  15. Feliform carnivores have a distinguished constitutive innate immune response

    PubMed Central

    Heinrich, Sonja K.; Wachter, Bettina; Aschenborn, Ortwin H. K.; Thalwitzer, Susanne; Melzheimer, Jörg; Hofer, Heribert; Czirják, Gábor Á.

    2016-01-01

    ABSTRACT Determining the immunological phenotype of endangered and threatened populations is important to identify those vulnerable to novel pathogens. Among mammals, members of the order Carnivora are particularly threatened by diseases. We therefore examined the constitutive innate immune system, the first line of protection against invading microbes, of six free-ranging carnivore species; the black-backed jackal (Canis mesomelas), the brown hyena (Hyena brunnea), the caracal (Caracal caracal), the cheetah (Acinonyx jubatus), the leopard (Panthera pardus) and the lion (Panthera leo) using a bacterial killing assay. The differences in immune responses amongst the six species were independent of their foraging behaviour, body mass or social organisation but reflected their phylogenetic relatedness. The bacterial killing capacity of black-backed jackals, a member of the suborder Caniformia, followed the pattern established for a wide variety of vertebrates. In contrast, the five representatives of the suborder Feliformia demonstrated a killing capacity at least an order of magnitude higher than any species reported previously, with a particularly high capacity in caracals and cheetahs. Our results suggest that the immunocompetence of threatened felids such as the cheetah has been underestimated and its assessment ought to consider both innate and adaptive components of the immune system. PMID:27044323

  16. Catalog of type specimens of recent mammals: Rodentia (Myomorpha, Anomaluromorpha, and Hystricomorpha) in the National Museum of Natural History, Smithsonian Institution

    USGS Publications Warehouse

    Fisher, Robert D.; Ludwig, Craig A.

    2014-01-01

    The type collection of Recent mammals in the Division of Mammals, National Museum of Natural History, Smithsonian Institution, contains 945 specimens bearing names of 931 species-group taxa of Rodentia (Myomorpha, Anomaluromorpha, and Hystricomorpha) as of August 2013. This catalog presents an annotated list of these holdings comprised of 905 holotypes, 16 lectotypes, 8 syntypes (48 specimens), and 2 neotypes. In addition, we include 44 specimens that are part of syntype series that should be in the collection but cannot be found or are now known to be in other collections. One hundred and ten of the names are new since the last type catalog covering these suborders A lectotype for Mus peruvianus Peale, 1848, is newly designated herein. Nine specimens previously reported were subsequently sent to the vertebrate paleontology collection and are not included here. Suborders and families are ordered as in Carleton and Musser; within families, currently recognized genera are arranged alphabetically; within each currently recognized genus, accounts are arranged alphabetically by original published name. Information in each account includes original name and abbreviated citation thereto, current name if other than original, citation for first use of current name combination for the taxon (or new name combination if used herein for the first time), type designation, U.S. National Museum catalog number(s), preparation, age and sex, date of collection and collector, original collector number, type locality, and remarks as appropriate. Digital photographs of each specimen will serve as a condition report and will be attached to each electronic specimen record.

  17. The first Chameleon transcriptome: comparative genomic analysis of the OXPHOS system reveals loss of COX8 in Iguanian lizards.

    PubMed

    Bar-Yaacov, Dan; Bouskila, Amos; Mishmar, Dan

    2013-01-01

    Recently, we found dramatic mitochondrial DNA divergence of Israeli Chamaeleo chamaeleon populations into two geographically distinct groups. We aimed to examine whether the same pattern of divergence could be found in nuclear genes. However, no genomic resource is available for any chameleon species. Here we present the first chameleon transcriptome, obtained using deep sequencing (SOLiD). Our analysis identified 164,000 sequence contigs of which 19,000 yielded unique BlastX hits. To test the efficacy of our sequencing effort, we examined whether the chameleon and other available reptilian transcriptomes harbored complete sets of genes comprising known biochemical pathways, focusing on the nDNA-encoded oxidative phosphorylation (OXPHOS) genes as a model. As a reference for the screen, we used the human 86 (including isoforms) known structural nDNA-encoded OXPHOS subunits. Analysis of 34 publicly available vertebrate transcriptomes revealed orthologs for most human OXPHOS genes. However, OXPHOS subunit COX8 (Cytochrome C oxidase subunit 8), including all its known isoforms, was consistently absent in transcriptomes of iguanian lizards, implying loss of this subunit during the radiation of this suborder. The lack of COX8 in the suborder Iguania is intriguing, since it is important for cellular respiration and ATP production. Our sequencing effort added a new resource for comparative genomic studies, and shed new light on the evolutionary dynamics of the OXPHOS system.

  18. Ultrastructure of chemoreceptive tarsal sensilla in an armored harvestman and evidence of olfaction across Laniatores (Arachnida, Opiliones).

    PubMed

    Gainett, Guilherme; Michalik, Peter; Müller, Carsten H G; Giribet, Gonzalo; Talarico, Giovanni; Willemart, Rodrigo H

    2017-01-10

    Harvestmen (Arachnida, Opiliones) are especially dependent on chemical cues and are often regarded as animals that rely mainly on contact chemoreception. Information on harvestman sensilla is scarce when compared to other arachnid orders, especially concerning internal morphology. Using scanning (SEM) and transmission (TEM) electron microscopy, we investigated tarsal sensilla on the distal tarsomeres (DT) of all leg pairs in Heteromitobates discolor (Laniatores, Gonyleptidae). Furthermore, we explored the typological diversity of sensilla present on the DT I and II in members of the suborder Laniatores, which include two thirds of the formally described opilionid fauna, using species from 17 families representing all main laniatorian lineages. Our data revealed that DT I and II of H. discolor are equipped with wall-pored falciform hairs (two types), wall-pored sensilla chaetica (two types) and tip-pored sensilla chaetica, while DT III and IV are mainly covered with trichomes (non-sensory) and tip-pored sensilla chaetica. The ultrastructural characteristics support an olfactory function for all wall-pored sensilla and a dual gustatory/mechanoreceptive function for tip-pored sensilla chaetica. Based on our comparative SEM survey, we show that wall-pored sensilla occur in all investigated Laniatores, demonstrating their widespread occurrence in the suborder and highlighting the importance of both legs I and II as the sensory appendages of laniatorean harvestmen. Our results provide the first morphological evidence for olfactory receptors in Laniatores and suggest that olfaction is more important for harvestmen than previously thought.

  19. Diversity of Nonribosomal Peptide Synthetase Genes in the Microbial Metagenomes of Marine Sponges

    PubMed Central

    Pimentel-Elardo, Sheila Marie; Grozdanov, Lubomir; Proksch, Sebastian; Hentschel, Ute

    2012-01-01

    Genomic mining revealed one major nonribosomal peptide synthetase (NRPS) phylogenetic cluster in 12 marine sponge species, one ascidian, an actinobacterial isolate and seawater. Phylogenetic analysis predicts its taxonomic affiliation to the actinomycetes and hydroxy-phenyl-glycine as a likely substrate. Additionally, a phylogenetically distinct NRPS gene cluster was discovered in the microbial metagenome of the sponge Aplysina aerophoba, which shows highest similarities to NRPS genes that were previously assigned, by ways of single cell genomics, to a Chloroflexi sponge symbiont. Genomic mining studies such as the one presented here for NRPS genes, contribute to on-going efforts to characterize the genomic potential of sponge-associated microbiota for secondary metabolite biosynthesis. PMID:22822366

  20. Marine actinobacteria: an important source of bioactive natural products.

    PubMed

    Manivasagan, Panchanathan; Kang, Kyong-Hwa; Sivakumar, Kannan; Li-Chan, Eunice C Y; Oh, Hyun-Myung; Kim, Se-Kwon

    2014-07-01

    Marine environment is largely an untapped source for deriving actinobacteria, having potential to produce novel, bioactive natural products. Actinobacteria are the prolific producers of pharmaceutically active secondary metabolites, accounting for about 70% of the naturally derived compounds that are currently in clinical use. Among the various actinobacterial genera, Actinomadura, Actinoplanes, Amycolatopsis, Marinispora, Micromonospora, Nocardiopsis, Saccharopolyspora, Salinispora, Streptomyces and Verrucosispora are the major potential producers of commercially important bioactive natural products. In this respect, Streptomyces ranks first with a large number of bioactive natural products. Marine actinobacteria are unique enhancing quite different biological properties including antimicrobial, anticancer, antiviral, insecticidal and enzyme inhibitory activities. They have attracted global in the last ten years for their ability to produce pharmaceutically active compounds. In this review, we have focused attention on the bioactive natural products isolated from marine actinobacteria, possessing unique chemical structures that may form the basis for synthesis of novel drugs that could be used to combat resistant pathogenic microorganisms.

  1. Actinobacteria mediated synthesis of nanoparticles and their biological properties: A review.

    PubMed

    Manivasagan, Panchanathan; Venkatesan, Jayachandran; Sivakumar, Kannan; Kim, Se-Kwon

    2016-01-01

    Nanotechnology is gaining tremendous attention in the present century due to its expected impact on many important areas such as medicine, energy, electronics, and space industries. In this context, actinobacterial biosynthesis of nanoparticles is a reliable, eco-friendly, and important aspect of green chemistry approach that interconnects microbial biotechnology and nanobiotechnology. Antibiotics produced by actinobacteria are popular in almost all the therapeutic measures and it is known that these microbes are also helpful in the biosynthesis of nanoparticles with good surface and size characteristics. In fact, actinobacteria are efficient producers of nanoparticles that show a range of biological properties, namely, antibacterial, antifungal, anticancer, anti-biofouling, anti-malarial, anti-parasitic, antioxidant, etc. This review describes the potential use of the actinobacteria as the novel sources for the biosynthesis of nanoparticles with improved biomedical applications.

  2. Metagenomic recovery of phage genomes of uncultured freshwater actinobacteria.

    PubMed

    Ghai, Rohit; Mehrshad, Maliheh; Megumi Mizuno, Carolina; Rodriguez-Valera, Francisco

    2017-01-01

    Low-GC Actinobacteria are among the most abundant and widespread microbes in freshwaters and have largely resisted all cultivation efforts. Consequently, their phages have remained totally unknown. In this work, we have used deep metagenomic sequencing to assemble eight complete genomes of the first tailed phages that infect freshwater Actinobacteria. Their genomes encode the actinobacterial-specific transcription factor whiB, frequently found in mycobacteriophages and also in phages infecting marine pelagic Actinobacteria. Its presence suggests a common and widespread strategy of modulation of host transcriptional machinery upon infection via this transcriptional switch. We present evidence that some whiB-carrying phages infect the acI lineage of Actinobacteria. At least one of them encodes the ADP-ribosylating component of the widespread bacterial AB toxins family (for example, clostridial toxin). We posit that the presence of this toxin reflects a 'trojan horse' strategy, providing protection at the population level to the abundant host microbes against eukaryotic predators.

  3. Cytoskeletal Proteins of Actinobacteria

    PubMed Central

    Letek, Michal; Fiuza, María; Villadangos, Almudena F.; Mateos, Luís M.; Gil, José A.

    2012-01-01

    Although bacteria are considered the simplest life forms, we are now slowly unraveling their cellular complexity. Surprisingly, not only do bacterial cells have a cytoskeleton but also the building blocks are not very different from the cytoskeleton that our own cells use to grow and divide. Nonetheless, despite important advances in our understanding of the basic physiology of certain bacterial models, little is known about Actinobacteria, an ancient group of Eubacteria. Here we review current knowledge on the cytoskeletal elements required for bacterial cell growth and cell division, focusing on actinobacterial genera such as Mycobacterium, Corynebacterium, and Streptomyces. These include some of the deadliest pathogens on earth but also some of the most prolific producers of antibiotics and antitumorals. PMID:22481946

  4. Complete genome sequence of Olsenella uli type strain (VPI D76D-27CT)

    SciTech Connect

    Goker, Markus; Held, Brittany; Lucas, Susan; Nolan, Matt; Yasawong, Montri; Glavina Del Rio, Tijana; Tice, Hope; Cheng, Jan-Fang; Bruce, David; Detter, J. Chris; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Ivanova, N; Mavromatis, K; Mikhailova, Natalia; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Rohde, Manfred; Sikorski, Johannes; Pukall, Rudiger; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-01-01

    Olsenella uli (Olsen et al. 1991) Dewhirst et al. 2001 is the type species of the genus Olsenella, which belongs to the actinobacterial family Coriobacteriaceae. The species is of interest because it is frequently isolated from dental plaque in periodontitis patients and can cause primary endodontic infection. The species is a Gram-positive, non-motile and non-sporulating bacterium. The strain described in this study has been isolated from human gingival crevices in 1982. This is the first completed sequence of the genus Olsenella and the fifth sequence from the family Coriobacteriaceae. The 2,051,896 bp long genome with its 1,795 protein-coding and 55 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  5. Complete genome sequence of Eggerthella lenta type strain (IPP VPI 0255T)

    SciTech Connect

    Saunders, Elizabeth H; Pukall, Rudiger; Birte, Abt; Lapidus, Alla L.; Glavina Del Rio, Tijana; Copeland, A; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Ivanova, N; Mavromatis, K; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Chain, Patrick S. G.; Meincke, Linda; Sims, David; Brettin, Tom; Detter, J. Chris; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Han, Cliff

    2009-01-01

    Eggerthella lenta (Eggerth 1935) Wade et al. 1999, emended W rdemann et al. 2009 is the type species of the genus Eggerthella, which belongs to the actinobacterial family Coriobacteriaceae. E. lenta is a Gram-positive, non-motile, non-sporulating pathogenic bacterium that can cause severe bacteremia. The strain described in this study has been isolated from a rectal tumor in 1935. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the genus Eggerthella, and the 3,632,260 bp long single replicon genome with its 3123 protein-coding and 58 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  6. Enzymology of aminoglycoside biosynthesis-deduction from gene clusters.

    PubMed

    Wehmeier, Udo F; Piepersberg, Wolfgang

    2009-01-01

    The classical aminoglycosides are, with very few exceptions, typically actinobacterial secondary metabolites with antimicrobial activities all mediated by inhibiting translation on the 30S subunit of the bacterial ribosome. Some chemically related natural products inhibit glucosidases by mimicking oligo-alpha-1,4-glucosides. The biochemistry of the aminoglycoside biosynthetic pathways is still a developing field since none of the pathways has been analyzed to completeness as yet. In this chapter we treat the enzymology of aminoglycoside biosyntheses as far as it becomes apparent from recent investigations based on the availability of DNA sequence data of biosynthetic gene clusters for all major structural classes of these bacterial metabolites. We give a more general overview of the field, including descriptions of some key enzymes in various aminoglycoside pathways, whereas in Chapter 20 provides a detailed account of the better-studied enzymology thus far known for the neomycin and butirosin pathways.

  7. Lentzea chajnantorensis sp. nov., an actinobacterium from a very high altitude Cerro Chajnantor gravel soil in northern Chile.

    PubMed

    Idris, Hamidah; Nouioui, Imen; Asenjo, Juan A; Bull, Alan T; Goodfellow, Michael

    2017-03-21

    The taxonomic position of a filamentous actinobacterial strain, isolate H45(T), recovered from a high altitude Atacama Desert gravel soil, was established using a polyphasic approach. The strain, which is known to produce novel dienes, has chemotaxonomic and morphological properties typical of the genus Lentzea and formed a distinct branch in the Lentzea 16S rRNA gene tree that is closely related to the type strain of Lentzea kentuckyensis. The two strains were distinguished using a combination of phenotypic properties and by a DNA:DNA relatedness value of 37.6 ± 4.0%. On the basis of these genotypic and phenotypic data it is proposed that isolate H45(T) (=NCIMB 4966(T) = NRRL B-65282(T)) be classified in the genus Lentzea as Lentzea chajnantorensis sp. nov.

  8. Production of Enzymes From Agricultural Wastes and Their Potential Industrial Applications.

    PubMed

    Bharathiraja, S; Suriya, J; Krishnan, M; Manivasagan, P; Kim, S-K

    2017-01-01

    Enzymatic hydrolysis is the significant technique for the conversion of agricultural wastes into valuable products. Agroindustrial wastes such as rice bran, wheat bran, wheat straw, sugarcane bagasse, and corncob are cheapest and plentifully available natural carbon sources for the production of industrially important enzymes. Innumerable enzymes that have numerous applications in industrial processes for food, drug, textile, and dye use have been produced from different types of microorganisms from agricultural wastes. Utilization of agricultural wastes offers great potential for reducing the production cost and increasing the use of enzymes for industrial purposes. This chapter focuses on economic production of actinobacterial enzymes from agricultural wastes to make a better alternative for utilization of biomass generated in million tons as waste annually.

  9. Bacterial recovery from ancient glacial ice.

    PubMed

    Christner, Brent C; Mosley-Thompson, Ellen; Thompson, Lonnie G; Reeve, John N

    2003-05-01

    Ice that forms the bottom 18 m of a 308 m ice core drilled from the Guliya ice cap on the Qinghan-Tibetan plateau in Western China is over 750000 years old and is the oldest glacial ice known to date. Fourteen bacterial isolates have been recovered from samples of this ice from approximately 296 m below the surface (mbs). Based on 16S rDNA sequences, these are members of the alpha- and beta-proteobacterial, actinobacterial and low-G + C Gram-positive bacterial lineages. 16S rDNA molecules have also been amplified directly, cloned and sequenced from the ice-core melt water. These originated from Pseudomonas and Acinetobacter gamma-proteobacterial species. These results demonstrate that bacteria can be recovered from water ice that has frozen for time periods relevant to biological survival through terrestrial ice ages or during interplanetary transport.

  10. Complete genome sequence of Intrasporangium calvumtype strain (7 KIPT)

    SciTech Connect

    Glavina Del Rio, Tijana; Chertkov, Olga; Yasawong, Montri; Lucas, Susan; Deshpande, Shweta; Cheng, Jan-Fang; Detter, J. Chris; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Ivanova, N; Mavromatis, K; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Rohde, Manfred; Pukall, Rudiger; Sikorski, Johannes; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lapidus, Alla L.

    2010-01-01

    Intrasporangium calvum Kalakoutskii et al. 1967 is the type species of the genus Intrasporangium, which belongs to the actinobacterial family Intrasporangiaceae. The species is a Gram-positive bacterium that forms a branching mycelium, which tends to break into irregular fragments. The mycelium of this strain may bear intercalary vesicles but does not contain spores. The strain described in this study is an airborne organism that was isolated from a school dining room in 1967. One particularly interesting feature of I. calvum is that the type of its menaquinone is different from all other representatives of the family Intrasporangiaceae. This is the first completed genome sequence from a member of the genus Intrasporangium and also the first sequence from the family Intrasporangiaceae. The 4,024,382 bp long genome with its 3,653 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  11. LC-MS-Based Metabolomics Study of Marine Bacterial Secondary Metabolite and Antibiotic Production in Salinispora arenicola

    PubMed Central

    Bose, Utpal; Hewavitharana, Amitha K.; Ng, Yi Kai; Shaw, Paul Nicholas; Fuerst, John A.; Hodson, Mark P.

    2015-01-01

    An LC-MS-based metabolomics approach was used to characterise the variation in secondary metabolite production due to changes in the salt content of the growth media as well as across different growth periods (incubation times). We used metabolomics as a tool to investigate the production of rifamycins (antibiotics) and other secondary metabolites in the obligate marine actinobacterial species Salinispora arenicola, isolated from Great Barrier Reef (GBR) sponges, at two defined salt concentrations and over three different incubation periods. The results indicated that a 14 day incubation period is optimal for the maximum production of rifamycin B, whereas rifamycin S and W achieve their maximum concentration at 29 days. A “chemical profile” link between the days of incubation and the salt concentration of the growth medium was shown to exist and reliably represents a critical point for selection of growth medium and harvest time. PMID:25574739

  12. Coffee husk composting: An investigation of the process using molecular and non-molecular tools

    PubMed Central

    Shemekite, Fekadu; Gómez-Brandón, María; Franke-Whittle, Ingrid H.; Praehauser, Barbara; Insam, Heribert; Assefa, Fassil

    2014-01-01

    Various parameters were measured during a 90-day composting process of coffee husk with cow dung (Pile 1), with fruit/vegetable wastes (Pile 2) and coffee husk alone (Pile 3). Samples were collected on days 0, 32 and 90 for chemical and microbiological analyses. C/N ratios of Piles 1 and 2 decreased significantly over the 90 days. The highest bacterial counts at the start of the process and highest actinobacterial counts at the end of the process (Piles 1 and 2) indicated microbial succession with concomitant production of compost relevant enzymes. Denaturing gradient gel electrophoresis of rDNA and COMPOCHIP microarray analysis indicated distinctive community shifts during the composting process, with day 0 samples clustering separately from the 32 and 90-day samples. This study, using a multi-parameter approach, has revealed differences in quality and species diversity of the three composts. PMID:24369846

  13. Complete genome sequence of Cryptobacterium curtum type strain (12-3T)

    SciTech Connect

    Mavromatis, Konstantinos; Pukall, Rudiger; Rohde, Christine; Sims, David; Brettin, Thomas; Kuske, Cheryl; Detter, John C.; Han, Cliff; Lapidus, Alla; Copeland, Alex; Glavina Del Rio, Tijana; Nolan, Matt; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ovchinnikova, Galina; Pati, Amrita; Ivanova, Natalia; Chen, Amy; Palaniappan, Krishna; Chain, Patrick; D'haeseleer, Patrik; Bristow, Jim; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Rohde, Manfred; Klenk, Hans-Peter; Kyrpides, Nikos C.

    2009-05-20

    Cryptobacterium curtum Nakazawa et al. 1999 is the type species of the genus, and is of phylogenetic interest because of its very distant and isolated position within the family Coriobacteriaceae. C. curtum is an asaccharolytic, opportunistic pathogen with a typical occurrence in the oral cavity, involved in dental and oral infections like periodontitis, inflammations and abscesses. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the actinobacterial family Coriobacteriaceae, and this 1,617,804 bp long single replicon genome with its 1364 protein-coding and 58 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  14. Termite Nests as an Abundant Source of Cultivable Actinobacteria for Biotechnological Purposes

    PubMed Central

    Sujada, Nikhom; Sungthong, Rungroch; Lumyong, Saisamorn

    2014-01-01

    A total of 118 actinobacterial isolates were collected from the three types of termite nests (mound, carton, and subterranean nests) to evaluate their potential as a source of bioactive actinobacteria with antimicrobial activity. The highest number (67 isolates) and generic abundance (7 known genera) of actinobacterial isolates were obtained from carton nests. Streptomyces was the dominant genus in each type of termite nest. In the non-Streptomyces group, Nocardia was the dominant genus detected in mound and carton nests, while Pseudonocardia was the dominant genus in subterranean nests. A discovery trend of novel species (<99% similarity in the 16S rRNA gene sequence) was also observed in the termite nests examined. Each type of termite nest housed >20% of bioactive actinobacteria that could inhibit the growth of at least one test organism, while 12 isolates, belonging to the genera Streptomyces, Amycolatopsis, Pseudonocardia, Micromonospora and Nocardia, exhibited distinct antimicrobial activities. Streptomyces sp. CMU-NKS-3 was the most distinct bioactive isolate. It was closely related to S. padanus MITKK-103T, which was confirmed by 99% similarities in their 16S rRNA gene sequences. The highest level of extracellular antimicrobial substances was produced by the isolate CMU-NKS-3, which was grown in potato dextrose broth and exhibited a wide range (6.10×10−4–1.25 mg mL−1) of minimum inhibitory concentrations against diverse pathogens. We concluded that termite nests are an abundant source of bioactive strains of cultivable actinobacteria for future biotechnological needs. PMID:24909709

  15. Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria.

    PubMed

    Selengut, Jeremy D; Haft, Daniel H

    2010-11-01

    Regimens targeting Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), require long courses of treatment and a combination of three or more drugs. An increase in drug-resistant strains of M. tuberculosis demonstrates the need for additional TB-specific drugs. A notable feature of M. tuberculosis is coenzyme F(420), which is distributed sporadically and sparsely among prokaryotes. This distribution allows for comparative genomics-based investigations. Phylogenetic profiling (comparison of differential gene content) based on F(420) biosynthesis nominated many actinobacterial proteins as candidate F(420)-dependent enzymes. Three such families dominated the results: the luciferase-like monooxygenase (LLM), pyridoxamine 5'-phosphate oxidase (PPOX), and deazaflavin-dependent nitroreductase (DDN) families. The DDN family was determined to be limited to F(420)-producing species. The LLM and PPOX families were observed in F(420)-producing species as well as species lacking F(420) but were particularly numerous in many actinobacterial species, including M. tuberculosis. Partitioning the LLM and PPOX families based on an organism's ability to make F(420) allowed the application of the SIMBAL (sites inferred by metabolic background assertion labeling) profiling method to identify F(420)-correlated subsequences. These regions were found to correspond to flavonoid cofactor binding sites. Significantly, these results showed that M. tuberculosis carries at least 28 separate F(420)-dependent enzymes, most of unknown function, and a paucity of flavin mononucleotide (FMN)-dependent proteins in these families. While prevalent in mycobacteria, markers of F(420) biosynthesis appeared to be absent from the normal human gut flora. These findings suggest that M. tuberculosis relies heavily on coenzyme F(420) for its redox reactions. This dependence and the cofactor's rarity may make F(420)-related proteins promising drug targets.

  16. Functional gene-based discovery of phenazines from the actinobacteria associated with marine sponges in the South China Sea.

    PubMed

    Karuppiah, Valliappan; Li, Yingxin; Sun, Wei; Feng, Guofang; Li, Zhiyong

    2015-07-01

    Phenazines represent a large group of nitrogen-containing heterocyclic compounds produced by the diverse group of bacteria including actinobacteria. In this study, a total of 197 actinobacterial strains were isolated from seven different marine sponge species in the South China Sea using five different culture media. Eighty-seven morphologically different actinobacterial strains were selected and grouped into 13 genera, including Actinoalloteichus, Kocuria, Micrococcus, Micromonospora, Mycobacterium, Nocardiopsis, Prauserella, Rhodococcus, Saccharopolyspora, Salinispora, Serinicoccus, and Streptomyces by the phylogenetic analysis of 16S rRNA gene. Based on the screening of phzE genes, ten strains, including five Streptomyces, two Nocardiopsis, one Salinispora, one Micrococcus, and one Serinicoccus were found to be potential for phenazine production. The level of phzE gene expression was highly expressed in Nocardiopsis sp. 13-33-15, 13-12-13, and Serinicoccus sp. 13-12-4 on the fifth day of fermentation. Finally, 1,6-dihydroxy phenazine (1) from Nocardiopsis sp. 13-33-15 and 13-12-13, and 1,6-dimethoxy phenazine (2) from Nocardiopsis sp. 13-33-15 were isolated and identified successfully based on ESI-MS and NMR analysis. The compounds 1 and 2 showed antibacterial activity against Bacillus mycoides SJ14, Staphylococcus aureus SJ51, Escherichia coli SJ42, and Micrococcus luteus SJ47. This study suggests that the integrated approach of gene screening and chemical analysis is an effective strategy to find the target compounds and lays the basis for the production of phenazine from the sponge-associated actinobacteria.

  17. The genome of a pathogenic rhodococcus: cooptive virulence underpinned by key gene acquisitions.

    PubMed

    Letek, Michal; González, Patricia; Macarthur, Iain; Rodríguez, Héctor; Freeman, Tom C; Valero-Rello, Ana; Blanco, Mónica; Buckley, Tom; Cherevach, Inna; Fahey, Ruth; Hapeshi, Alexia; Holdstock, Jolyon; Leadon, Desmond; Navas, Jesús; Ocampo, Alain; Quail, Michael A; Sanders, Mandy; Scortti, Mariela M; Prescott, John F; Fogarty, Ursula; Meijer, Wim G; Parkhill, Julian; Bentley, Stephen D; Vázquez-Boland, José A

    2010-09-30

    We report the genome of the facultative intracellular parasite Rhodococcus equi, the only animal pathogen within the biotechnologically important actinobacterial genus Rhodococcus. The 5.0-Mb R. equi 103S genome is significantly smaller than those of environmental rhodococci. This is due to genome expansion in nonpathogenic species, via a linear gain of paralogous genes and an accelerated genetic flux, rather than reductive evolution in R. equi. The 103S genome lacks the extensive catabolic and secondary metabolic complement of environmental rhodococci, and it displays unique adaptations for host colonization and competition in the short-chain fatty acid-rich intestine and manure of herbivores--two main R. equi reservoirs. Except for a few horizontally acquired (HGT) pathogenicity loci, including a cytoadhesive pilus determinant (rpl) and the virulence plasmid vap pathogenicity island (PAI) required for intramacrophage survival, most of the potential virulence-associated genes identified in R. equi are conserved in environmental rhodococci or have homologs in nonpathogenic Actinobacteria. This suggests a mechanism of virulence evolution based on the cooption of existing core actinobacterial traits, triggered by key host niche-adaptive HGT events. We tested this hypothesis by investigating R. equi virulence plasmid-chromosome crosstalk, by global transcription profiling and expression network analysis. Two chromosomal genes conserved in environmental rhodococci, encoding putative chorismate mutase and anthranilate synthase enzymes involved in aromatic amino acid biosynthesis, were strongly coregulated with vap PAI virulence genes and required for optimal proliferation in macrophages. The regulatory integration of chromosomal metabolic genes under the control of the HGT-acquired plasmid PAI is thus an important element in the cooptive virulence of R. equi.

  18. Unexpected Abundance of Coenzyme F420-Dependent Enzymes in Mycobacterium tuberculosis and Other Actinobacteria▿ †

    PubMed Central

    Selengut, Jeremy D.; Haft, Daniel H.

    2010-01-01

    Regimens targeting Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), require long courses of treatment and a combination of three or more drugs. An increase in drug-resistant strains of M. tuberculosis demonstrates the need for additional TB-specific drugs. A notable feature of M. tuberculosis is coenzyme F420, which is distributed sporadically and sparsely among prokaryotes. This distribution allows for comparative genomics-based investigations. Phylogenetic profiling (comparison of differential gene content) based on F420 biosynthesis nominated many actinobacterial proteins as candidate F420-dependent enzymes. Three such families dominated the results: the luciferase-like monooxygenase (LLM), pyridoxamine 5′-phosphate oxidase (PPOX), and deazaflavin-dependent nitroreductase (DDN) families. The DDN family was determined to be limited to F420-producing species. The LLM and PPOX families were observed in F420-producing species as well as species lacking F420 but were particularly numerous in many actinobacterial species, including M. tuberculosis. Partitioning the LLM and PPOX families based on an organism's ability to make F420 allowed the application of the SIMBAL (sites inferred by metabolic background assertion labeling) profiling method to identify F420-correlated subsequences. These regions were found to correspond to flavonoid cofactor binding sites. Significantly, these results showed that M. tuberculosis carries at least 28 separate F420-dependent enzymes, most of unknown function, and a paucity of flavin mononucleotide (FMN)-dependent proteins in these families. While prevalent in mycobacteria, markers of F420 biosynthesis appeared to be absent from the normal human gut flora. These findings suggest that M. tuberculosis relies heavily on coenzyme F420 for its redox reactions. This dependence and the cofactor's rarity may make F420-related proteins promising drug targets. PMID:20675471

  19. Termite nests as an abundant source of cultivable actinobacteria for biotechnological purposes.

    PubMed

    Sujada, Nikhom; Sungthong, Rungroch; Lumyong, Saisamorn

    2014-01-01

    A total of 118 actinobacterial isolates were collected from the three types of termite nests (mound, carton, and subterranean nests) to evaluate their potential as a source of bioactive actinobacteria with antimicrobial activity. The highest number (67 isolates) and generic abundance (7 known genera) of actinobacterial isolates were obtained from carton nests. Streptomyces was the dominant genus in each type of termite nest. In the non-Streptomyces group, Nocardia was the dominant genus detected in mound and carton nests, while Pseudonocardia was the dominant genus in subterranean nests. A discovery trend of novel species (<99% similarity in the 16S rRNA gene sequence) was also observed in the termite nests examined. Each type of termite nest housed >20% of bioactive actinobacteria that could inhibit the growth of at least one test organism, while 12 isolates, belonging to the genera Streptomyces, Amycolatopsis, Pseudonocardia, Micromonospora and Nocardia, exhibited distinct antimicrobial activities. Streptomyces sp. CMU-NKS-3 was the most distinct bioactive isolate. It was closely related to S. padanus MITKK-103T, which was confirmed by 99% similarities in their 16S rRNA gene sequences. The highest level of extracellular antimicrobial substances was produced by the isolate CMU-NKS-3, which was grown in potato dextrose broth and exhibited a wide range (6.10×10(-4)-1.25 mg mL(-1)) of minimum inhibitory concentrations against diverse pathogens. We concluded that termite nests are an abundant source of bioactive strains of cultivable actinobacteria for future biotechnological needs.

  20. Actinophytocola algeriensis sp. nov., an actinobacterium isolated from Saharan soil.

    PubMed

    Bouznada, Khaoula; Bouras, Noureddine; Schumann, Peter; Spröer, Cathrin; Sabaou, Nasserdine; Klenk, Hans-Peter

    2016-05-04

    Throughout our investigations for new actinobacterial taxa, a new actinobacterial strain, designated MB20T, was isolated from a Saharan soil sample, collected in Mzab region (Ghardaïa province, South Algeria). In order to reveal its taxonomic position, the novel strain was characterized following a polyphasic taxonomic approach. It was noticed that strain MB20T produce white branched and fragmented substrate mycelium with no aerial mycelium on the most tested media. Chemotaxonomic and phylogenetic studies clearly demonstrated that the strain MB20T belonged to the family Pseudonocardiaceae and was closely related to the genus Actinophytocola. Cell-wall hydrolysates contained meso-diaminopimelic acid but not glycine, and whole-cell hydrolysates contained galactose, glucose and ribose. The diagnostic phospholipid was phosphatidylethanolamine. Mycolic acids were not detected while the predominant fatty acid was found to be iso-branched hexadecanoate (iso-C16 : 0). The major menaquinone was MK-9(H4). Results of the 16S rRNA gene sequence comparison revealed that strain MB20T shared the highest degree of similarity with Actinophytocola gilvus DSM 45828T (98.5 %), Actinophytocola corallina DSM 45659T (98.0 %) and Actinophytocola timorensis DSM 45660T (97.5 %). However, DNA-DNA hybridization studies showed only 32.9 % similarity with A. timorensis, 23.7 % similarity with A. gilvus and 17.9 % similarity with A. corallina. On the basis of phenotypic characteristics, 16S rRNA gene sequence comparisons and DNA-DNA hybridization, strain MB20T revealed to be a novel species of the genus Actinophytocola, for which the name Actinophytocola algeriensis sp. nov. (type strain MB20T =DSM 46746T = CECT 8960T) is proposed.

  1. The Genome of a Pathogenic Rhodococcus: Cooptive Virulence Underpinned by Key Gene Acquisitions

    PubMed Central

    Letek, Michal; González, Patricia; MacArthur, Iain; Rodríguez, Héctor; Freeman, Tom C.; Valero-Rello, Ana; Blanco, Mónica; Buckley, Tom; Cherevach, Inna; Fahey, Ruth; Hapeshi, Alexia; Holdstock, Jolyon; Leadon, Desmond; Navas, Jesús; Ocampo, Alain; Quail, Michael A.; Sanders, Mandy; Scortti, Mariela M.; Prescott, John F.; Fogarty, Ursula; Meijer, Wim G.; Parkhill, Julian; Bentley, Stephen D.; Vázquez-Boland, José A.

    2010-01-01

    We report the genome of the facultative intracellular parasite Rhodococcus equi, the only animal pathogen within the biotechnologically important actinobacterial genus Rhodococcus. The 5.0-Mb R. equi 103S genome is significantly smaller than those of environmental rhodococci. This is due to genome expansion in nonpathogenic species, via a linear gain of paralogous genes and an accelerated genetic flux, rather than reductive evolution in R. equi. The 103S genome lacks the extensive catabolic and secondary metabolic complement of environmental rhodococci, and it displays unique adaptations for host colonization and competition in the short-chain fatty acid–rich intestine and manure of herbivores—two main R. equi reservoirs. Except for a few horizontally acquired (HGT) pathogenicity loci, including a cytoadhesive pilus determinant (rpl) and the virulence plasmid vap pathogenicity island (PAI) required for intramacrophage survival, most of the potential virulence-associated genes identified in R. equi are conserved in environmental rhodococci or have homologs in nonpathogenic Actinobacteria. This suggests a mechanism of virulence evolution based on the cooption of existing core actinobacterial traits, triggered by key host niche–adaptive HGT events. We tested this hypothesis by investigating R. equi virulence plasmid-chromosome crosstalk, by global transcription profiling and expression network analysis. Two chromosomal genes conserved in environmental rhodococci, encoding putative chorismate mutase and anthranilate synthase enzymes involved in aromatic amino acid biosynthesis, were strongly coregulated with vap PAI virulence genes and required for optimal proliferation in macrophages. The regulatory integration of chromosomal metabolic genes under the control of the HGT–acquired plasmid PAI is thus an important element in the cooptive virulence of R. equi. PMID:20941392

  2. Comparative genomics reveals evidence of marine adaptation in Salinispora species

    PubMed Central

    2012-01-01

    Background Actinobacteria represent a consistent component of most marine bacterial communities yet little is known about the mechanisms by which these Gram-positive bacteria adapt to life in the marine environment. Here we employed a phylogenomic approach to identify marine adaptation genes in marine Actinobacteria. The focus was on the obligate marine actinomycete genus Salinispora and the identification of marine adaptation genes that have been acquired from other marine bacteria. Results Functional annotation, comparative genomics, and evidence of a shared evolutionary history with bacteria from hyperosmotic environments were used to identify a pool of more than 50 marine adaptation genes. An Actinobacterial species tree was used to infer the likelihood of gene gain or loss in accounting for the distribution of each gene. Acquired marine adaptation genes were associated with electron transport, sodium and ABC transporters, and channels and pores. In addition, the loss of a mechanosensitive channel gene appears to have played a major role in the inability of Salinispora strains to grow following transfer to low osmotic strength media. Conclusions The marine Actinobacteria for which genome sequences are available are broadly distributed throughout the Actinobacterial phylogenetic tree and closely related to non-marine forms suggesting they have been independently introduced relatively recently into the marine environment. It appears that the acquisition of transporters in Salinispora spp. represents a major marine adaptation while gene loss is proposed to play a role in the inability of this genus to survive outside of the marine environment. This study reveals fundamental differences between marine adaptations in Gram-positive and Gram-negative bacteria and no common genetic basis for marine adaptation among the Actinobacteria analyzed. PMID:22401625

  3. Prevalence of lysogeny among soil bacteria and presence of 16S rRNA and trzN genes in viral-community DNA.

    PubMed

    Ghosh, Dhritiman; Roy, Krishnakali; Williamson, Kurt E; White, David C; Wommack, K Eric; Sublette, Kerry L; Radosevich, Mark

    2008-01-01

    Bacteriophages are very abundant in the biosphere, and viral infection is believed to affect the activity and genetic diversity of bacterial communities in aquatic environments. Lysogenic conversion, for example, can improve host fitness and lead to phage-mediated horizontal gene transfer. However, little is known about lysogeny and transduction in the soil environment. In this study we employed atrazine-impregnated Bio-Sep beads (a cell immobilization matrix) to sample active microbiota from soils with prior pesticide exposure history. Once recovered from soil, the bead communities were induced with mitomycin C (MC), and viral and bacterial abundances were determined to evaluate the incidence of inducible prophage in soil bacteria. The inducible fraction calculated within bead communities was high (ca. 85%) relative to other studies in aquatic and sedimentary environments. Moreover, the bacterial genes encoding 16S rRNA and trzN, a chlorohydrolase gene responsible for dehalogenation of atrazine, were detected by PCR in the viral DNA fraction purified from MC-induced bead communities. A diverse collection of actinobacterial 16S rRNA gene sequences occurred within the viral DNA fraction of induced, water-equilibrated beads. Similar results were observed in induced atrazine-equilibrated beads, where 77% of the cloned sequences were derived from actinobacterial lineages. Heterogeneous 16S rRNA gene sequences consisting of fragments from two different taxa were detected in the clone libraries. The results suggest that lysogeny is a prevalent reproductive strategy among soil bacteriophages and that the potential for horizontal gene transfer via transduction is significant in soil microbial communities.

  4. Variation in Pseudonocardia antibiotic defence helps govern parasite-induced morbidity in Acromyrmex leaf-cutting ants.

    PubMed

    Poulsen, Michael; Cafaro, Matías J; Erhardt, Daniel P; Little, Ainslie E F; Gerardo, Nicole M; Tebbets, Brad; Klein, Bruce S; Currie, Cameron R

    2010-08-01

    Host-parasite associations are potentially shaped by evolutionary reciprocal selection dynamics, in which parasites evolve to overcome host defences and hosts are selected to counteract these through the evolution of new defences. This is expected to result in variation in parasite-defence interactions, and the evolution of resistant parasites causing increased virulence. Fungus-growing ants maintain antibiotic-producing Pseudonocardia (Actinobacteria) that aid in protection against specialized parasites of the ants' fungal gardens, and current evidence indicates that both symbionts have been associated with the ants for millions of years. Here we examine the extent of variation in the defensive capabilities of the ant-actinobacterial association against Escovopsis (parasite-defence interactions), and evaluate how variation impacts colonies of fungus-growing ants. We focus on five species of Acromyrmex leaf-cutting ants, crossing 12 strains of Pseudonocardia with 12 strains of Escovopsis in a Petri plate bioassay experiment, and subsequently conduct subcolony infection experiments using resistant and non-resistant parasite strains. Diversity in parasite-defence interactions, including pairings where the parasites are resistant, suggests that chemical variation in the antibiotics produced by different actinobacterial strains are responsible for the observed variation in parasite susceptibility. By evaluating the role this variation plays during infection, we show that infection of ant subcolonies with resistant parasite strains results in significantly higher parasite-induced morbidity with respect to garden biomass loss. Our findings thus further establish the role of Pseudonocardia-derived antibiotics in helping defend the ants' fungus garden from the parasite Escovopsis, and provide evidence that small molecules can play important roles as antibiotics in a natural system.

  5. Microbial Communities Show Parallels at Sites with Distinct Litter and Soil Characteristics▿†

    PubMed Central

    Sagova-Mareckova, Marketa; Omelka, Marek; Cermak, Ladislav; Kamenik, Zdenek; Olsovska, Jana; Hackl, Evelyn; Kopecky, Jan; Hadacek, Franz

    2011-01-01

    Plant and microbial community composition in connection with soil chemistry determines soil nutrient cycling. The study aimed at demonstrating links between plant and microbial communities and soil chemistry occurring among and within four sites: two pine forests with contrasting soil pH and two grasslands of dissimilar soil chemistry and vegetation. Soil was characterized by C and N content, particle size, and profiles of low-molecular-weight compounds determined by high-performance liquid chromatography (HPLC) of soil extracts. Bacterial and actinobacterial community composition was assessed by terminal restriction fragment length polymorphism (T-RFLP) and cloning followed by sequencing. Abundances of bacteria, fungi, and actinobacteria were determined by quantitative PCR. In addition, a pool of secondary metabolites was estimated by erm resistance genes coding for rRNA methyltransferases. The sites were characterized by a stable proportion of C/N within each site, while on a larger scale, the grasslands had a significantly lower C/N ratio than the forests. A Spearman's test showed that soil pH was correlated with bacterial community composition not only among sites but also within each site. Bacterial, actinobacterial, and fungal abundances were related to carbon sources while T-RFLP-assessed microbial community composition was correlated with the chemical environment represented by HPLC profiles. Actinobacteria community composition was the only studied microbial characteristic correlated to all measured factors. It was concluded that the microbial communities of our sites were influenced primarily not only by soil abiotic characteristics but also by dominant litter quality, particularly, by percentage of recalcitrant compounds. PMID:21926225

  6. The dynamic proliferation of CanSINEs mirrors the complex evolution of Feliforms

    PubMed Central

    2014-01-01

    Background Repetitive short interspersed elements (SINEs) are retrotransposons ubiquitous in mammalian genomes and are highly informative markers to identify species and phylogenetic associations. Of these, SINEs unique to the order Carnivora (CanSINEs) yield novel insights on genome evolution in domestic dogs and cats, but less is known about their role in related carnivores. In particular, genome-wide assessment of CanSINE evolution has yet to be completed across the Feliformia (cat-like) suborder of Carnivora. Within Feliformia, the cat family Felidae is composed of 37 species and numerous subspecies organized into eight monophyletic lineages that likely arose 10 million years ago. Using the Felidae family as a reference phylogeny, along with representative taxa from other families of Feliformia, the origin, proliferation and evolution of CanSINEs within the suborder were assessed. Results We identified 93 novel intergenic CanSINE loci in Feliformia. Sequence analyses separated Feliform CanSINEs into two subfamilies, each characterized by distinct RNA polymerase binding motifs and phylogenetic associations. Subfamily I CanSINEs arose early within Feliformia but are no longer under active proliferation. Subfamily II loci are more recent, exclusive to Felidae and show evidence for adaptation to extant RNA polymerase activity. Further, presence/absence distributions of CanSINE loci are largely congruent with taxonomic expectations within Feliformia and the less resolved nodes in the Felidae reference phylogeny present equally ambiguous CanSINE data. SINEs are thought to be nearly impervious to excision from the genome. However, we observed a nearly complete excision of a CanSINEs locus in puma (Puma concolor). In addition, we found that CanSINE proliferation in Felidae frequently targeted existing CanSINE loci for insertion sites, resulting in tandem arrays. Conclusions We demonstrate the existence of at least two SINE families within the Feliformia suborder, one

  7. Regional diversity of amphipoda in the Caribbean Sea.

    PubMed

    Martín, Alberto; Díaz, Yusbelly; Miloslavich, Patricia; Escobar-Briones, Elva; Guerra-García, José Manuel; Ortiz, Manuel; Valencia, Bellineth; Giraldo, Alan; Klein, Eduardo

    2013-12-01

    The order Amphipoda is one of the most diverse within Peracarids, and comprises 6950 described marine species. Amphipod research in the Caribbean Sea began in the late 1800s, but has increased significantly since 1980. In this study, we analized the amphipod biodiversity (Caprellidea, Gammaridea, Hyperiidea, and Ingolfiellidea) of the Caribbean Sea. For this, we compiled available data on species diversity of marine amphipods (data bases: WoRMS and OBIS and published species lists) into a comprehensive taxonomic list by country for the ecoregions of the Caribbean. Additionally, we analized the relative contribution of each country to regional diversity and the rate of discovery of new species. The Caribbean amphipod fauna is composed of 535 species within 236 genera and 73 families for the higher taxon. The Western Caribbean ecoregion holds the largest diversity (282 species), while the Eastern Caribbean recorded the lowest one (73). Mexico and Venezuela recorded the largest number of species with 266 and 206, respectively. Twelve countries had less than 50 species. The richest suborder is the Gammaridea with 381 species followed by the suborder Hyperiidea with 116. From the total of 535 amphipod species reported for the Caribbean region, 218 have the Caribbean as the holotype locality, and 132 are endemic (about 25% of the total). Areas of higher diversity seem to be concentrated along the Mexican Caribbean, Cuba and the Northern coast of South America (Venezuela-Colombia); however, such pattern is most likely reflecting local collection efforts and taxonomic expertise rather than actual distribution. Knowledge of amphipod species is mostly limited to shallow, near-shore waters, with little infonnation available on the deep sea fauna. Regional research priorities for this group should be focused on completing shallow water coastal inventories of species in Central America and the Greater and Lesser Antilles. In addition, sampling the deep sea ecosystems should

  8. The type-specimens of Caraboidea beetles (Coleoptera, Adephaga) deposited in the collections of the I.I. Schmalhausen Institute of Zoology, National Academy of Sciences of Ukraine.

    PubMed

    Putshkov, Alexander V; Martynov, Alexander V

    2017-03-01

    A catalogue of type specimens of species and subspecies of caraboid beetles, tiger-beetles here treated as family Cicindelidae, and ground-beetles (Carabidae) of suborder Adephaga deposited in the I.I. Schmalhausen Institute of Zoology NAS of Ukraine is provided. For all type-specimens original photos of each specimen (with label) and label data are given in the original spelling (translated to English if the original label was in Cyrillic alphabet). In some cases data concerning the current status of taxons are discussed. Nominal taxa names are alphabethically listed within each family. Altogether, 372 type specimens of 133 taxa names (species and subspecies) are included in the catalogue: 15 holotypes, 344 paratypes (120 species and subspecies) and 13 specimens (9 taxa) with other type status.

  9. Phylogenetic relationships of the marine Haplosclerida (Phylum Porifera) employing ribosomal (28S rRNA) and mitochondrial (cox1, nad1) gene sequence data.

    PubMed

    Redmond, Niamh E; Raleigh, Jean; van Soest, Rob W M; Kelly, Michelle; Travers, Simon A A; Bradshaw, Brian; Vartia, Salla; Stephens, Kelly M; McCormack, Grace P

    2011-01-01

    The systematics of the poriferan Order Haplosclerida (Class Demospongiae) has been under scrutiny for a number of years without resolution. Molecular data suggests that the order needs revision at all taxonomic levels. Here, we provide a comprehensive view of the phylogenetic relationships of the marine Haplosclerida using many species from across the order, and three gene regions. Gene trees generated using 28S rRNA, nad1 and cox1 gene data, under maximum likelihood and Bayesian approaches, are highly congruent and suggest the presence of four clades. Clade A is comprised primarily of species of Haliclona and Callyspongia, and clade B is comprised of H. simulans and H. vansoesti (Family Chalinidae), Amphimedon queenslandica (Family Niphatidae) and Tabulocalyx (Family Phloeodictyidae), Clade C is comprised primarily of members of the Families Petrosiidae and Niphatidae, while Clade D is comprised of Aka species. The polyphletic nature of the suborders, families and genera described in other studies is also found here.

  10. [Microarthropods from the altiplanic andean steppe, with focus on oribatid species (Oribatida: Acarina)].

    PubMed

    Covarrubias, Rene

    2009-01-01

    In soils under seven types of high altitude, native vegetation and one plantation in the northernmost Chilean Altiplanic region, 20 microarthropod orders or suborders were found, including 21 oribatid mite species. Seven of these species are first mentioned for Chile. No oribatid mites were found in soils far from vegetation. Data are given as average densities (n masculine ind./1000 ml), accounting for plant preference, geographical distribution and updated taxonomic status for each species. Ten oribatid species form a group of Andean altiplanic steppe fauna also found in Peru and Bolivia. Other three species have been also found in different austral ecosystems in Argentina, and a group of eight species seems to be cosmopolitan.

  11. Development of remote sensing techniques capable of delineating soils as an aid to soil survey

    NASA Technical Reports Server (NTRS)

    Coleman, T. L.; Montgomery, O. L.

    1988-01-01

    Eighty-one benchmark soils from Alabama, Georgia, Florida, Tennessee, and Mississippi were evaluated to determine the feasibility of spectrally differentiating among soil categories. Relationships among spectral properties that occur between soils and within soils were examined, using discriminant analysis. Soil spectral data were obtained from air-dried samples using an Exotech Model 20C field spectroradiometer (0.37 to 2.36 microns). Differentiating among the orders, suborders, great groups, and subgroups using reflectance spectra achieved varying percentages of accuracy. Six distinct reflectance curve forms were developed from the air-dried samples based on the shape and presence or absence of adsorption bands. Iron oxide and organic matter content were the dominant soil parameters affecting the spectral characteristics for differentiating among and between these soils.

  12. Peltogasterella sensuru n. sp. (Crustacea: Cirripedia: Rhizocephala) from off Okinawa Island (Ryukyu Archipelago, Japan) with remarks on its single brood externae.

    PubMed

    Yoshida, Ryuta; Hirose, Mamiko; Hirose, Euichi

    2015-09-01

    Peltogasterella sensuru n. sp. infests Pagurixus hermit crabs inhabiting rocky shores off Okinawa Island (Ryukyu Archipelago, Japan). This species is clearly distinguishable from Peltogasterella gracilis (Boschma, 1927): the stalk emerges from the middle part of the externa in the present species and P. sulcata (Lilljeborg, 1859), while the stalk in P. gracilis emerges from the posterior end of the externae. The new species differs from P. sulcata based on the morphology of the mantle aperture. Peltogasterella sensuru n. sp. repeatedly produces single brood externae that have not been previously observed in species belonging to the suborder Kentrogonida Delage, 1884. We also determined partial sequences of the COI gene and 16S rRNA gene of the new species for use as molecular markers for species identification.

  13. A megafauna's microfauna: gastrointestinal parasites of New Zealand's extinct moa (Aves: Dinornithiformes).

    PubMed

    Wood, Jamie R; Wilmshurst, Janet M; Rawlence, Nicolas J; Bonner, Karen I; Worthy, Trevor H; Kinsella, John M; Cooper, Alan

    2013-01-01

    WE PERFORM THE FIRST MULTIDISCIPLINARY STUDY OF PARASITES FROM AN EXTINCT MEGAFAUNAL CLADE USING COPROLITES FROM THE NEW ZEALAND MOA (AVES: Dinornithiformes). Ancient DNA and microscopic analyses of 84 coprolites deposited by four moa species (South Island giant moa, Dinornis robustus; little bush moa, Anomalopteryx didiformis; heavy-footed moa, Pachyornis elephantopus; and upland moa, Megalapteryx didinus) reveal an array of gastrointestinal parasites including coccidians (Cryptosporidium and members of the suborder Eimeriorina), nematodes (Heterakoidea, Trichostrongylidae, Trichinellidae) and a trematode (Echinostomida). Parasite eggs were most prevalent and diverse in coprolites from lowland sites, where multiple sympatric moa species occurred and host density was therefore probably higher. Morphological and phylogenetic evidence supports a possible vicariant Gondwanan origin for some of the moa parasites. The discovery of apparently host-specific parasite taxa suggests paleoparasitological studies of megafauna coprolites may provide useful case-studies of coextinction.

  14. Mycalina: another crack in the Poecilosclerida framework.

    PubMed

    Hajdu, Eduardo; de Paula, Thiago S; Redmond, Niamh E; Cosme, Bruno; Collins, Allen G; Lôbo-Hajdu, Gisele

    2013-09-01

    This is the first phylogenetic analysis integrating both morphological and molecular data of the sponge suborder Mycalina (Poecilosclerida), which was erected in 1994. A cladistic analysis of morphology supported the monophyly of Cladorhizidae (including Euchelipluma), Guitarridae (excluding Euchelipluma), Isodictyidae, Latrunculiidae, and Podospongiidae but rejected monophyly for Desmacellidae, Esperiopsidae, Hamacanthidae, and Mycalidae. Analyses of partial 16S and partial 28S rRNA datasets combined, as well as that of a complete 18S rDNA dataset, suggest that Mycalina is not monophyletic; Biemnidae is only distantly related to other poecilosclerids; Merlia and Desmacella branch near the base of a diverse Poecilosclerida clade; Mycalidae is monophyletic (excluding Mycale [Anomomycale] titubans in 18S); and Esperiopsidae and Isodictyidae form a clade. Analyses of the two molecular datasets differed on the monophyly of Podospongiidae and about the relationship of Podospongiidae to Isodictyidae + Esperiopsidae.

  15. Neotropical harvestmen (Arachnida, Opiliones) use sexually dimorphic glands to spread chemicals in the environment.

    PubMed

    Fernandes, Nathália da Silva; Willemart, Rodrigo Hirata

    2014-04-01

    Sexually dimorphic glands have convergently appeared in animals and are often responsible for the production of pheromones. In the suborder Laniatores of the order Opiliones (Arachnida), glands of such type are widespread, but there is not a single paper on how they are used. Using Scanning Electron Microscopy and a behavioral approach, we describe glandular openings and how these glands are used, in the harvestmen Gryne perlata and Gryne coccinelloides (Cosmetidae). Males of these two species have glandular openings on the metatarsi of legs I and on the metatarsi IV. Males were shown rubbing the glands of the metatarsi I against their other legs, whereas glands on the metatarsi IV are gently touched on the substrate or rubbed either against other legs, or against the substrate. Not all behaviors were seen in both species.

  16. Chemical structure and anticoagulant activity of highly pyruvylated sulfated galactans from tropical green seaweeds of the order Bryopsidales.

    PubMed

    Arata, Paula X; Quintana, Irene; Canelón, Dilsia J; Vera, Beatriz E; Compagnone, Reinaldo S; Ciancia, Marina

    2015-05-20

    Sulfated and pyruvylated galactans were isolated from three tropical species of the Bryopsidales, Penicillus capitatus, Udotea flabellum, and Halimeda opuntia. They represent the only important sulfated polysaccharides present in the cell walls of these highly calcified seaweeds of the suborder Halimedineae. Their structural features were studied by chemical analyses and NMR spectroscopy. Their backbone comprises 3-, 6-, and 3,6-linkages, constituted by major amounts of 3-linked 4,6-O-(1'-carboxy)ethylidene-d-galactopyranose units in part sulfated on C-2. Sulfation on C-2 was not found in galactans from other seaweeds of this order. In addition, a complex sulfation pattern, comprising also 4-, 6-, and 4,6-disulfated galactose units was found. A fraction from P. capitatus, F1, showed a moderate anticoagulant activity, evaluated by general coagulation tests and also kinetics of fibrin formation was assayed. Besides, preliminary results suggest that one of the possible mechanisms involved is direct thrombin inhibition.

  17. Characterisation of Major Histocompatibility Complex Class I in the Australian Cane Toad, Rhinella marina

    PubMed Central

    Lillie, Mette; Shine, Richard; Belov, Katherine

    2014-01-01

    The Major Histocompatibility Complex (MHC) class I is a highly variable gene family that encodes cell-surface receptors vital for recognition of intracellular pathogens and initiation of immune responses. The MHC class I has yet to be characterised in bufonid toads (Order: Anura; Suborder: Neobatrachia; Family: Bufonidae), a large and diverse family of anurans. Here we describe the characterisation of a classical MHC class I gene in the Australian cane toad, Rhinella marina. From 25 individuals sampled from the Australian population, we found only 3 alleles at this classical class I locus. We also found large number of class I alpha 1 alleles, implying an expansion of class I loci in this species. The low classical class I genetic diversity is likely the result of repeated bottleneck events, which arose as a result of the cane toad's complex history of introductions as a biocontrol agent and its subsequent invasion across Australia. PMID:25093458

  18. Comparative cytogenetics of Auchenorrhyncha (Hemiptera, Homoptera): a review

    PubMed Central

    Kuznetsova, Valentina; Aguin-Pombo, Dora

    2015-01-01

    Abstract A comprehensive review of cytogenetic features is provided for the large hemipteran suborder Auchenorrhyncha, which currently contains approximately 42,000 valid species. This review is based on the analysis of 819 species, 483 genera, and 31 families representing all presently recognized Auchenorrhyncha superfamilies, e.i. Cicadoidea (cicadas), Cercopoidea (spittle bugs), Membracoidea (leafhoppers and treehoppers), Myerslopioidea (ground-dwelling leafhoppers), and Fulgoroidea (planthoppers). History and present status of chromosome studies are described, as well as the structure of chromosomes, chromosome counts, trends and mechanisms of evolution of karyotypes and sex determining systems, their variation at different taxonomic levels and most characteristic (modal) states, occurrence of parthenogenesis, polyploidy, B-chromosomes and chromosome rearrangements, and methods used for cytogenetic analysis of Auchenorrhyncha. PMID:26807037

  19. Phylogenetic affinity of tree shrews to Glires is attributed to fast evolution rate.

    PubMed

    Lin, Jiannan; Chen, Guangfeng; Gu, Liang; Shen, Yuefeng; Zheng, Meizhu; Zheng, Weisheng; Hu, Xinjie; Zhang, Xiaobai; Qiu, Yu; Liu, Xiaoqing; Jiang, Cizhong

    2014-02-01

    Previous phylogenetic analyses have led to incongruent evolutionary relationships between tree shrews and other suborders of Euarchontoglires. What caused the incongruence remains elusive. In this study, we identified 6845 orthologous genes between seventeen placental mammals. Tree shrews and Primates were monophyletic in the phylogenetic trees derived from the first or/and second codon positions whereas tree shrews and Glires formed a monophyly in the trees derived from the third or all codon positions. The same topology was obtained in the phylogeny inference using the slowly and fast evolving genes, respectively. This incongruence was likely attributed to the fast substitution rate in tree shrews and Glires. Notably, sequence GC content only was not informative to resolve the controversial phylogenetic relationships between tree shrews, Glires, and Primates. Finally, estimation in the confidence of the tree selection strongly supported the phylogenetic affiliation of tree shrews to Primates as a monophyly.

  20. Total Mercury in Six Antarctic Notothenioid Fishes.

    PubMed

    Wintle, Nathan J P; Sleadd, Isaac M; Gundersen, Deke T; Kohl, Kristina; Buckley, Bradley A

    2015-11-01

    We analyzed white muscle samples from six species of Antarctic fish (suborder Notothenioidei) collected in 2011 from McMurdo Sound, Ross Sea, Antarctica, to assess levels of total mercury (THg). Gymnodraco acuticeps and Trematomus bernacchii exhibited the highest concentrations of THg followed by Trematomus pennellii, Trematomus nicolai, Trematomus newnesi and Pagothenia borchgrevinki, (71.3, 53.9±32.1, 45.8±27.3, 37.2±18.6, 35.7±23.6, and 21.9±2.8 ng/g wet weight, respectively). The results from this study suggest that THg has the potential to bioaccumulate from various marine Antarctic ecosystems into biota.

  1. Biology bacteriocyte-associated endosymbionts of plant sap-sucking insects.

    PubMed

    Baumann, Paul

    2005-01-01

    Psyllids, whiteflies, aphids, and mealybugs are members of the suborder Sternorrhyncha and share a common property, namely the utilization of plant sap as their food source. Each of these insect groups has an obligatory association with a different prokaryotic endosymbiont, and the association is the result of a single infection followed by maternal, vertical transmission of the endosymbionts. The result of this association is the domestication of the free-living bacterium to serve the purposes of the host, namely the synthesis of essential amino acids. This domestication is probably in all cases accompanied by a major reduction in genome size. The different properties of the genomes and fragments of the genomes of these endosymbionts suggest that there are different constraints on the permissible evolutionary changes that are probably a function of the gene repertoire of the endosymbiont ancestor and the gene losses that occurred during the reduction of genome size.

  2. Cryptosporidium is more closely related to the gregarines than to coccidia as shown by phylogenetic analysis of apicomplexan parasites inferred using small-subunit ribosomal RNA gene sequences.

    PubMed

    Carreno, R A; Martin, D S; Barta, J R

    1999-11-01

    The phylogenetic placement of gregarine parasites (Apicomplexa: Gregarinasina) within the Apicomplexa was derived by comparison of small-subunit ribosomal RNA gene sequences. Gregarine sequences were obtained from Gregarina niphandrodes Clopton, Percival, and Janovy, 1991, and Monocystis agilis Stein, 1848 (Eugregarinorida Léger 1900), as well as from Ophriocystis elektroscirrha McLaughlin and Myers, 1970 (Neogregarinorida Grassé 1953). The sequences were aligned with several other gregarine and apicomplexan sequences from GenBank and the resulting data matrix analyzed by parsimony and maximum-likelihood methods. The gregarines form a monophyletic clade that is a sister group to Cryptosporidium spp. The gregarine/ Cryptosporidium clade is separate from the other major apicomplexan clade containing the coccidia, adeleids, piroplasms, and haemosporinids. The trees indicate that the genus Cryptosporidium has a closer phylogenetic affinity with the gregarines than with the coccidia. These results do not support the present classification of the Cryptosporidiidae in the suborder Eimerioirina Léger, 1911.

  3. The majority of vitamin A is transported as retinyl esters in the blood of most carnivores.

    PubMed

    Schweigert, F J; Ryder, O A; Rambeck, W A; Zucker, H

    1990-01-01

    1. In canines and mustelides total vitamin A was 10-50 times higher compared to other species due to a high amount of retinyl esters (40-99% of total vitamin A) in blood plasma. The dominant vitamin A ester was in most species retinyl stearate. 2. In Ursidae, Procyonidae, Viveridae and Felidae, total vitamin A was much lower. When present, however, retinyl esters also represented 10-65% of total vitamin A in plasma. 3. Only retinol was detected in plasma of the family, Hyaenidae, and the suborder, Pinnipedia. 4. In maned wolf cubs it was found that retinol, retinyl esters and alpha-tocopherol increased with the age of the animals, reaching values comparable to adult animals at the age of 5 months.

  4. The sense of smell in Odonata: an electrophysiological screening.

    PubMed

    Piersanti, Silvana; Frati, Francesca; Conti, Eric; Rebora, Manuela; Salerno, Gianandrea

    2014-11-01

    Volatile chemicals mediate a great range of intra- and interspecific signalling and information in insects. Olfaction has been widely investigated mostly in Neoptera while the knowledge of this sense in most basal insects such as Paleoptera (Odonata and Ephemeroptera) is still poor. In the present study we show the results of an electrophysiological screening on two model species, Libellula depressa (Libellulidae) and Ischnura elegans (Coenagrionidae), representatives of the two Odonata suborders Anisoptera and Zygoptera, with the aim to deep the knowledge on the sense of smell of this insect order. The antennal olfactory sensory neurons (OSNs) of these two species responded to the same 22 compounds (out of 48 chemicals belonging to different functional groups) encompassing mostly amines, carboxylic acids or aldehydes and belonging to green leaf volatiles, vertebrate related volatiles and volatiles emitted by standing waters bacteria. The properties of Odonata OSNs are very similar to those of ionotropic receptors (IRs) expressing OSNs in other insects.

  5. Complete mitochondrial genome of an enigmatic dragonfly, Epiophlebia superstes (Odonata, Epiophlebiidae).

    PubMed

    Wang, Jo-Fan; Chen, Ming-Yu; Chaw, Shu-Miaw; Morii, Yuta; Yoshimura, Mayumi; Sota, Teiji; Lin, Chung-Ping

    2015-01-01

    This study reported the 15,435 bp-long complete mitochondrial genome of the relict Epiophlebia superstes (Odonata, Epiophlebiidae), an enigmatic dragonfly of the paraphyletic 'Anisozygoptera' possessing characteristics similar to members of both extant odonate suborders, the Zygoptera and the Anisoptera. This mitogenome comprises the common set of 37 genes and an A + T-rich control region, and has a gene arrangement identical to those of all available odonates. The genome contains three non-coding inter-genic spacers (s1-s3), which occurs in all of other known odonates, but it lacks the inter-genic spacer s5 typically found in the Anisoptera. This result suggests that E. superstes possesses a mitogenmic organization more closely related to that of the Zygoptera than that of the Anizoptera.

  6. Horizontal Gene Transfer of Pectinases from Bacteria Preceded the Diversification of Stick and Leaf Insects

    PubMed Central

    Shelomi, Matan; Danchin, Etienne G. J.; Heckel, David; Wipfler, Benjamin; Bradler, Sven; Zhou, Xin; Pauchet, Yannick

    2016-01-01

    Genes acquired by horizontal transfer are increasingly being found in animal genomes. Understanding their origin and evolution requires knowledge about the phylogenetic relationships from both source and recipient organisms. We used RNASeq data and respective assembled transcript libraries to trace the evolutionary history of polygalacturonase (pectinase) genes in stick insects (Phasmatodea). By mapping the distribution of pectinase genes on a Polyneoptera phylogeny, we identified the transfer of pectinase genes from known phasmatodean gut microbes into the genome of an early euphasmatodean ancestor that took place between 60 and 100 million years ago. This transfer preceded the rapid diversification of the suborder, enabling symbiont-free pectinase production that would increase the insects’ digestive efficiency and reduce dependence on microbes. Bacteria-to-insect gene transfer was thought to be uncommon, however the increasing availability of large-scale genomic data may change this prevailing notion. PMID:27210832

  7. Adaptive radiation of venomous marine snail lineages and the accelerated evolution of venom peptide genes

    PubMed Central

    Olivera, Baldomero M.; Watkins, Maren; Bandyopadhyay, Pradip; Imperial, Julita S.; de la Cotera, Edgar P. Heimer; Aguilar, Manuel B.; Vera, Estuardo López; Concepcion, Gisela P.; Lluisma, Arturo

    2012-01-01

    An impressive biodiversity (>10,000 species) of marine snails (suborder Toxoglossa or superfamily Conoidea) have complex venoms, containing ca. 100 biologically active, disulfide-rich peptides. In the genus Conus, the most intensively investigated toxoglossan lineage (~500 species), a small set of venom gene superfamilies undergo rapid sequence hyperdiversification within their mature toxin regions. Each major lineage of Toxoglossa has its own distinct set of venom gene superfamilies. Two recently identified venom gene superfamilies are expressed in the large Turridae clade, but not in Conus. Thus, as major venomous molluscan clades expand, a small set of lineage specific venom gene superfamilies undergo accelerated evolution. The juxtaposition of extremely conserved signal sequences with hypervariable mature peptide regions is unprecedented and raises the possibility that in these gene superfamilies, the signal sequences are conserved as a result of an essential role they play in enabling rapid sequence evolution of the region of the gene that encodes the active toxin. PMID:22954218

  8. Evolutionary biology of harvestmen (Arachnida, Opiliones).

    PubMed

    Giribet, Gonzalo; Sharma, Prashant P

    2015-01-07

    Opiliones are one of the largest arachnid orders, with more than 6,500 species in 50 families. Many of these families have been erected or reorganized in the last few years since the publication of The Biology of Opiliones. Recent years have also seen an explosion in phylogenetic work on Opiliones, as well as in studies using Opiliones as test cases to address biogeographic and evolutionary questions more broadly. Accelerated activity in the study of Opiliones evolution has been facilitated by the discovery of several key fossils, including the oldest known Opiliones fossil, which represents a new, extinct suborder. Study of the group's biology has also benefited from rapid accrual of genomic resources, particularly with respect to transcriptomes and functional genetic tools. The rapid emergence and utility of Phalangium opilio as a model for evolutionary developmental biology of arthropods serve as demonstrative evidence of a new area of study in Opiliones biology, made possible through transcriptomic data.

  9. Guyanagarika, a new ectomycorrhizal genus of Agaricales from the Neotropics.

    PubMed

    Sánchez-García, Marisol; Henkel, Terry W; Aime, Mary Catherine; Smith, Matthew E; Matheny, Patrick Brandon

    2016-12-01

    A new genus and three new species of Agaricales are described from the Pakaraima Mountains of Guyana in the central Guiana Shield. All three of these new species fruit on the ground in association with species of the ectomycorrhizal (ECM) tree genus Dicymbe (Fabaceae subfam. Caesalpinioideae) and one species has been shown to form ectomycorrhizas. Multi-locus molecular phylogenetic analyses place Guyanagarika gen. nov. within the Catathelasma clade, a lineage in the suborder Tricholomatineae of the Agaricales. We formally recognize this 'Catathelasma clade' as an expanded family Catathelasmataceae that includes the genera Callistosporium, Catathelasma, Guyanagarika, Macrocybe, Pleurocollybia, and Pseudolaccaria. Within the Catathelasmataceae, Catathelasma and Guyanagarika represent independent origins of the ectomycorrhizal habit. Guyanagarika is the first documented case of an ECM Agaricales genus known only from the Neotropics.

  10. [What gene and chromosomes say about the origin and evolution of insects and other arthropods].

    PubMed

    Lukhtanov, V A; Kuznetsova, V G

    2010-09-01

    At the turn of the 21st century, the use of molecular and molecular cytogenetic methods led to revolutionary advances in systematics of insects and other arthropods. Analysis of nuclear and mitochondrial genes, as well as investigation of structural rearrangements in the mitochondrial chromosome convincingly supported the Pancrustacea hypothesis, according to which insects originated directly from crustaceans, whereas myriapods are not closely related to them. The presence of the specific telomeric motif TTAGG confirmed the monophyletic origin of arthropods (Arthropoda) and the assignment of tongue worms (Pentastomida) to this type. Several different types of telomeric sequences have been found within the class of insects. Investigation of the molecular organization of these sequences may shed light on the relationships between the orders Diptera, Siphonaptera, and Mecoptera and on the origin of such enigmatic groups as the orders Strepsiptera, Zoraptera and suborder Coleorrhyncha.

  11. Mitochondrial genome sequences of Nematocera (lower Diptera): evidence of rearrangement following a complete genome duplication in a winter crane fly.

    PubMed

    Beckenbach, Andrew T

    2012-01-01

    The complete mitochondrial DNA sequences of eight representatives of lower Diptera, suborder Nematocera, along with nearly complete sequences from two other species, are presented. These taxa represent eight families not previously represented by complete mitochondrial DNA sequences. Most of the sequences retain the ancestral dipteran mitochondrial gene arrangement, while one sequence, that of the midge Arachnocampa flava (family Keroplatidae), has an inversion of the trnE gene. The most unusual result is the extensive rearrangement of the mitochondrial genome of a winter crane fly, Paracladura trichoptera (family Trichocera). The pattern of rearrangement indicates that the mechanism of rearrangement involved a tandem duplication of the entire mitochondrial genome, followed by random and nonrandom loss of one copy of each gene. Another winter crane fly retains the ancestral diperan gene arrangement. A preliminary mitochondrial phylogeny of the Diptera is also presented.

  12. The complete mitochondrial genome of the Hoffmann's two-toed sloth (Choloepus hoffmanni).

    PubMed

    Song, Xiaolei; Chen, Lingyun; Chen, Xi; Jia, Huijue

    2016-09-01

    The Hoffmann's two-toed sloth (Choloepus hoffmanni), a member of Folivora suborder, is found in the rainforest canopy of South America. Both the Hoffmann's two-toed sloth and human belong to Eutheria subclass. In this study, the complete mitochondrial genome of C. hoffmanni is reported . The whole mitochondrial genome is 16 466 bp in length, including 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. Comparison between the mitochondrial genome of the C. hoffmanni and that of its congener Choloepus didactylus revealed a high similarity in their gene sequences. We also constructed a phylogenetic tree on the complete mitochondrial genomes of these two species and other 14 closely related species to show their phylogenic relationship. To conclude, we analyzed the complete mitochondrial genome of C. hoffmanni and its phylogenic relationship with other related species, which would facilitate our understanding of the evolution of eutherian mitochondrial genome.

  13. Asynchronous extinction of late Quaternary sloths on continents and islands.

    PubMed

    Steadman, David W; Martin, Paul S; MacPhee, Ross D E; Jull, A J T; McDonald, H Gregory; Woods, Charles A; Iturralde-Vinent, Manuel; Hodgins, Gregory W L

    2005-08-16

    Whatever the cause, it is extraordinary that dozens of genera of large mammals became extinct during the late Quaternary throughout the Western Hemisphere, including 90% of the genera of the xenarthran suborder Phyllophaga (sloths). Radiocarbon dates directly on dung, bones, or other tissue of extinct sloths place their "last appearance" datum at approximately 11,000 radiocarbon years before present (yr BP) or slightly less in North America, approximately 10,500 yr BP in South America, and approximately 4,400 yr BP on West Indian islands. This asynchronous situation is not compatible with glacial-interglacial climate change forcing these extinctions, especially given the great elevational, latitudinal, and longitudinal variation of the sloth-bearing continental sites. Instead, the chronology of last appearance of extinct sloths, whether on continents or islands, more closely tracks the first arrival of people.

  14. First Biosynthetic pathway of 1-hepten-3-one in Iporangaia pustulosa (Opiliones)

    PubMed Central

    Rocha, Daniele F. O.; Wouters, Felipe C.; Machado, Glauco; Marsaioli, Anita J.

    2013-01-01

    Arthropods produce a great variety of natural compounds, many of which have unexplored biosynthesis. Among the armored harvestmen (Arachnida: Opiliones) of the suborder Laniatores, the defensive gland exudates contain vinyl ketones and other constituents of supposed polyketide origin. We have studied the biosynthesis of 1-hepten-3-one in the Neotropical harvestman Iporangaia pustulosa by feeding individuals with 13C-labeled precursors, demonstrating its mixed acetate/propionate origin. 13C NMR spectroscopy showed an unusual labeling pattern suggesting different propionate sources for starting and extender units. Our analysis also indicates the presence of methylmalonyl-CoA mutase, converting acetate into propionyl-CoA via succinyl-CoA, together with other C3 unit routes. This is the first biosynthetic study of alkyl vinyl ketones in arthropods. Our results shed light on the origin and diversification of chemical compounds in a major arthropod group. PMID:24193576

  15. New Acotylea (Polycladida, Platyhelminthes) from the east coast of the North Atlantic Ocean with special mention of the Iberian littoral.

    PubMed

    Noreña, Carolina; Rodríguez, Jorge; Pérez, Jacinto; Almon, Bruno

    2015-11-03

    Polyclad species diversity, although generally well known for European North Atlantic waters, is nearly unknown for the Iberian Peninsula. The "Ría de Arousa", located on the Atlantic coast of Galicia (Spain), is a place where many positive biological factors for species biodiversity converge. Therefore, it is an ideal location to study polyclad diversity. This research, which describes new records and new species, contributes to the knowledge of the distribution of Polycladida (Platyhelminthes), particularly of the suborder Acotylea, in the Atlantic waters of the Iberian Peninsula. The new records include the re-descriptions of Cryptocelis compacta Lang, 1884, Stylochus neapolitanus (Delle Chiaje, 1841-1844) and Discocelis tigrina (Blanchard, 1847), while the two newly described species are Hoploplana elisabelloi n. sp. and Armatoplana celta n. sp.

  16. Supergroup F Wolbachia bacteria parasitise lice (Insecta: Phthiraptera).

    PubMed

    Covacin, Catherine; Barker, Stephen C

    2007-02-01

    We studied six species of lice from three of the four suborders of lice. These lice were infected with Wolbachia bacteria from supergroups A and F. This is the first report of an infection of supergroup F Wolbachia in lice. To date, Wolbachia from supergroup F have been found in filarial nematodes, Mansonella spp., and, rarely, in insects. We inferred the phylogeny of the Wolbachia from lice and representatives of all Wolbachia supergroups, with nucleotide sequences from the small subunit ribosomal RNA gene (SSU rRNA). There was no evidence of congruence between the taxon of louse and the Wolbachia bacteria that infect lice. There is no evidence that Wolbachia and their louse hosts co-evolved at least at the level of Wolbachia supergroups. We propose a novel mechanism for the horizontal transfer of Wolbachia between different species of lice from birds: transfer of Wolbachia during phoresis by hippoboscid flies.

  17. Demodex castoris sp. nov. (Acari: Demodecidae) parasitizing Castor fiber (Rodentia), and other parasitic arthropods associated with Castor spp.

    PubMed

    Izdebska, Joanna N; Fryderyk, Sławomira; Rolbiecki, Leszek

    2016-02-11

    A new species of demodecid mite, Demodex castoris sp. nov. (Acari: Prostigmata: Demodecidae), is described based on adult stages from the skin of the nasal region of the Eurasian beaver Castor fiber Linnaeus, 1758, collected in Poland. This is the first detection of a representative demodecid mite in rodents of the suborder Castorimorpha and also represents the first detection of a skin mite in Eurasian beavers. The new species is a small skin mite (average 173 µm in length) characterized by sexual dimorphism related to body proportions. D. castoris sp. nov. was observed in 4 out of 6 beavers examined (66.6%), with a mean intensity of 10.8 and an intensity range of 2-23 ind. host(-1). This paper also contains a checklist of parasitic arthropods known from Castor spp.

  18. Complete genome sequence of Haliangium ochraceum type strain (SMP-2T)

    SciTech Connect

    Ivanova, N; Daum, Chris; Lang, Elke; Abt, Birte; Kopitz, marcus; Saunders, Elizabeth H; Lapidus, Alla L.; Lucas, Susan; Glavina Del Rio, Tijana; Nolan, Matt; Tice, Hope; Copeland, A; Cheng, Jan-Fang; Chen, Feng; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Mavromatis, K; Pati, Amrita; Mikhailova, Natalia; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Detter, J. Chris; Brettin, Thomas S; Rohde, Manfred; Goker, Markus; Bristow, James; Markowitz, Victor; Eisen, Jonathan; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-01-01

    Haliangium ochraceum Fudou et al. 2002 is the type species of the genus Haliangium in the myxococcal family Haliangiaceae . Members of the genus Haliangium are the first halophilic myxobacterial taxa described. The cells of the species follow a multicellular lifestyle in highly organized biofilms, called swarms, they decompose bacterial and yeast cells as most myxobacteria do. The fruiting bodies contain particularly small coccoid myxospores. H. ochraceum encodes the first actin homologue identified in a bacterial genome. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the myxococcal suborder Nannocystineae, and the 9,446,314 bp long single replicon genome with its 6,898 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  19. Complete genome sequence of Haliangium ochraceum type strain (SMP-2).

    PubMed

    Ivanova, Natalia; Daum, Chris; Lang, Elke; Abt, Birte; Kopitz, Markus; Saunders, Elizabeth; Lapidus, Alla; Lucas, Susan; Glavina Del Rio, Tijana; Nolan, Matt; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Chen, Feng; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Mavromatis, Konstantinos; Pati, Amrita; Mikhailova, Natalia; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D; Detter, John C; Brettin, Thomas; Rohde, Manfred; Göker, Markus; Bristow, Jim; Markowitz, Victor; Eisen, Jonathan A; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-01-28

    Haliangium ochraceum Fudou et al. 2002 is the type species of the genus Haliangium in the myxococcal family 'Haliangiaceae'. Members of the genus Haliangium are the first halophilic myxobacterial taxa described. The cells of the species follow a multicellular lifestyle in highly organized biofilms, called swarms, they decompose bacterial and yeast cells as most myxobacteria do. The fruiting bodies contain particularly small coccoid myxospores. H. ochraceum encodes the first actin homologue identified in a bacterial genome. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the myxococcal suborder Nannocystineae, and the 9,446,314 bp long single replicon genome with its 6,898 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  20. Complete genome sequence of Haliangium ochraceum type strain (SMP-2T)

    PubMed Central

    Ivanova, Natalia; Daum, Chris; Lang, Elke; Abt, Birte; Kopitz, Markus; Saunders, Elizabeth; Lapidus, Alla; Lucas, Susan; Glavina Del Rio, Tijana; Nolan, Matt; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Chen, Feng; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Mavromatis, Konstantinos; Pati, Amrita; Mikhailova, Natalia; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Detter, John C.; Brettin, Thomas; Rohde, Manfred; Göker, Markus; Bristow, Jim; Markowitz, Victor; Eisen, Jonathan A.; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter

    2010-01-01

    Haliangium ochraceum Fudou et al. 2002 is the type species of the genus Haliangium in the myxococcal family ‘Haliangiaceae’. Members of the genus Haliangium are the first halophilic myxobacterial taxa described. The cells of the species follow a multicellular lifestyle in highly organized biofilms, called swarms, they decompose bacterial and yeast cells as most myxobacteria do. The fruiting bodies contain particularly small coccoid myxospores. H. ochraceum encodes the first actin homologue identified in a bacterial genome. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the myxococcal suborder Nannocystineae, and the 9,446,314 bp long single replicon genome with its 6,898 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:21304682

  1. Asynchronous extinction of late Quaternary sloths on continents and islands

    PubMed Central

    Steadman, David W.; Martin, Paul S.; MacPhee, Ross D. E.; Jull, A. J. T.; McDonald, H. Gregory; Woods, Charles A.; Iturralde-Vinent, Manuel; Hodgins, Gregory W. L.

    2005-01-01

    Whatever the cause, it is extraordinary that dozens of genera of large mammals became extinct during the late Quaternary throughout the Western Hemisphere, including 90% of the genera of the xenarthran suborder Phyllophaga (sloths). Radiocarbon dates directly on dung, bones, or other tissue of extinct sloths place their “last appearance” datum at ≈11,000 radiocarbon years before present (yr BP) or slightly less in North America, ≈10,500 yr BP in South America, and ≈4,400 yr BP on West Indian islands. This asynchronous situation is not compatible with glacial–interglacial climate change forcing these extinctions, especially given the great elevational, latitudinal, and longitudinal variation of the sloth-bearing continental sites. Instead, the chronology of last appearance of extinct sloths, whether on continents or islands, more closely tracks the first arrival of people. PMID:16085711

  2. The complete mitochondrial DNA sequence of the short mackerel (Rastrelliger brachysoma), and its phylogenetic position within Scombroidei, Perciformes.

    PubMed

    Jondeung, Amnuay; Karinthanyakit, Wirangrong

    2010-04-01

    In order to support studies of short mackerel population genetic structure in the Gulf of Thailand and phylogenetic relationships, the mitochondrial genome of the short mackerel, Rastrelliger brachysoma, has recently been determined by a partial cloning technique, long PCR with three pairs of newly designed primers and primer walking sequencing. The complete mitochondrial genome is 16,539 bp in length and contains 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes) and a control region (CR) as in other bony fishes. Within the 845-bp CR, we identified several conserved motifs. The phylogeny obtained by Bayesian analyses based on two nucleotide datasets corresponding to the cytb and nd2 mitochondrial genes strongly support the inclusion of R. brachysoma within the monophyletic tribe of Scombrini in the family Scombridae. The obtained phylogeny also reveals high-statistical support for the existence of two distinct groups indicating that Scombroidei and Xiphioidei are two separate suborders.

  3. First Biosynthetic pathway of 1-hepten-3-one in Iporangaia pustulosa (Opiliones)

    NASA Astrophysics Data System (ADS)

    Rocha, Daniele F. O.; Wouters, Felipe C.; Machado, Glauco; Marsaioli, Anita J.

    2013-11-01

    Arthropods produce a great variety of natural compounds, many of which have unexplored biosynthesis. Among the armored harvestmen (Arachnida: Opiliones) of the suborder Laniatores, the defensive gland exudates contain vinyl ketones and other constituents of supposed polyketide origin. We have studied the biosynthesis of 1-hepten-3-one in the Neotropical harvestman Iporangaia pustulosa by feeding individuals with 13C-labeled precursors, demonstrating its mixed acetate/propionate origin. 13C NMR spectroscopy showed an unusual labeling pattern suggesting different propionate sources for starting and extender units. Our analysis also indicates the presence of methylmalonyl-CoA mutase, converting acetate into propionyl-CoA via succinyl-CoA, together with other C3 unit routes. This is the first biosynthetic study of alkyl vinyl ketones in arthropods. Our results shed light on the origin and diversification of chemical compounds in a major arthropod group.

  4. Mites (acari) infesting commensal rats in Suez Canal zone, Egypt.

    PubMed

    el Kady, G A; Shoukry, A; Ragheb, D A; el Said, A M; Habib, K S; Morsy, T A

    1995-08-01

    Mites are arthropods distinguished from ticks by usually being microscopical in size and have a hypostome unarmed with tooth-like anchoring processes. They are group in a number of suborders, each with super-families and families including many genera of medical and economic importance. In this paper, commensal rodents (Rattus norvegicus, R. r. alexandrinus and R. r. frugivorous) were surveyed in the Suez Canal Zone for their acari ectoparasites. Four species of mites were recovered. In a descending order of mite indices, they were Eulaelaps stabularis (4.83 on 6 rats), Laelaps nuttalli (3.11 on 27 rats), Ornithonyssus bacoti (1.66 on 9 rats) and Dermanyssus gallinae (0.66 on 24 rats). The overall mite indices in the three governorates were 3.66 in Suez, 2.82 in Ismailia and zero in Port Said. The medical and economic importance of the mites were discussed.

  5. Effects of the Distribution of Female Primates on the Number of Males

    PubMed Central

    Carnes, Laurel Mariah; Nunn, Charles L.; Lewis, Rebecca J.

    2011-01-01

    The spatiotemporal distribution of females is thought to drive variation in mating systems, and hence plays a central role in understanding animal behavior, ecology and evolution. Previous research has focused on investigating the links between female spatiotemporal distribution and the number of males in haplorhine primates. However, important questions remain concerning the importance of spatial cohesion, the generality of the pattern across haplorhine and strepsirrhine primates, and the consistency of previous findings given phylogenetic uncertainty. To address these issues, we examined how the spatiotemporal distribution of females influences the number of males in primate groups using an expanded comparative dataset and recent advances in Bayesian phylogenetic and statistical methods. Specifically, we investigated the effect of female distributional factors (female number, spatial cohesion, estrous synchrony, breeding season duration and breeding seasonality) on the number of males in primate groups. Using Bayesian approaches to control for uncertainty in phylogeny and the model of trait evolution, we found that the number of females exerted a strong influence on the number of males in primate groups. In a multiple regression model that controlled for female number, we found support for temporal effects, particularly involving female estrous synchrony: the number of males increases when females are more synchronously receptive. Similarly, the number of males increases in species with shorter birth seasons, suggesting that greater breeding seasonality makes defense of females more difficult for male primates. When comparing primate suborders, we found only weak evidence for differences in traits between haplorhines and strepsirrhines, and including suborder in the statistical models did not affect our conclusions or give compelling evidence for different effects in haplorhines and strepsirrhines. Collectively, these results demonstrate that male monopolization

  6. Complete mitochondrial genomes of three neobatrachian anurans: a case study of divergence time estimation using different data and calibration settings.

    PubMed

    Igawa, Takeshi; Kurabayashi, Atsushi; Usuki, Chisako; Fujii, Tamotsu; Sumida, Masayuki

    2008-01-15

    We sequenced the whole mitochondrial (mt) genomes of three neobatrachian species: Japanese tree frog Hyla japonica, Japanese common toad Bufo japonicus, and narrow-mouthed toad Microhyla okinavensis. The gene arrangements of these genomes diverged from that of basal anurans (suborder Archaeobatrachia), but are the same as that of the members of derived frogs (i.e., superfamily Hyloidae and Ranoidae in suborder Neobatrachia), suggesting the one-time occurrence of a gene rearrangement event in an ancestral lineage of derived anurans. Furthermore, several distinct repeat motifs including putative termination-associated sequences (TASs) and conserved sequence blocks (CSBs) were observed in the control regions (CRs) of B. japonicus and H. japonica, while no repeat motifs were found in that of M. okinavensis. Phylogenetic analyses using both nucleotide and amino acid data of mt genes support monophyly of neobatrachians. The estimated divergence time based on amino acid data with multiple reference points suggests that the three living amphibian orders may have originated in the Carboniferous period, and that the divergences of anurans had occurred between the Permian and Tertiary periods. We also checked the influence of the data types and the settings of reference times on divergence time estimation. The resultant divergence times estimated from several datasets and reference time settings suggest that the substitution saturation of nucleotide data may lead to overestimated (i.e., older) branching times, especially for early divergent taxa. We also found a highly accelerated substitution rate in neobatrachian mt genes, and fast substitution possibly resulted in overestimation. To correct this erroneous estimation, it is efficient to apply several reference points among neobatrachians.

  7. Genome-wide bioinformatics analysis of steroid metabolism-associated genes in Nocardioides simplex VKM Ac-2033D.

    PubMed

    Shtratnikova, Victoria Y; Schelkunov, Mikhail I; Fokina, Victoria V; Pekov, Yury A; Ivashina, Tanya; Donova, Marina V

    2016-08-01

    Actinobacteria comprise diverse groups of bacteria capable of full degradation, or modification of different steroid compounds. Steroid catabolism has been characterized best for the representatives of suborder Corynebacterineae, such as Mycobacteria, Rhodococcus and Gordonia, with high content of mycolic acids in the cell envelope, while it is poorly understood for other steroid-transforming actinobacteria, such as representatives of Nocardioides genus belonging to suborder Propionibacterineae. Nocardioides simplex VKM Ac-2033D is an important biotechnological strain which is known for its ability to introduce ∆(1)-double bond in various 1(2)-saturated 3-ketosteroids, and perform convertion of 3β-hydroxy-5-ene steroids to 3-oxo-4-ene steroids, hydrolysis of acetylated steroids, reduction of carbonyl groups at C-17 and C-20 of androstanes and pregnanes, respectively. The strain is also capable of utilizing cholesterol and phytosterol as carbon and energy sources. In this study, a comprehensive bioinformatics genome-wide screening was carried out to predict genes related to steroid metabolism in this organism, their clustering and possible regulation. The predicted operon structure and number of candidate gene copies paralogs have been estimated. Binding sites of steroid catabolism regulators KstR and KstR2 specified for N. simplex VKM Ac-2033D have been calculated de novo. Most of the candidate genes grouped within three main clusters, one of the predicted clusters having no analogs in other actinobacteria studied so far. The results offer a base for further functional studies, expand the understanding of steroid catabolism by actinobacteria, and will contribute to modifying of metabolic pathways in order to generate effective biocatalysts capable of producing valuable bioactive steroids.

  8. The adipokinetic hormones of Odonata: a phylogenetic approach.

    PubMed

    Gäde, Gerd; Marco, Heather G

    2005-03-01

    Adipokinetic neuropeptides from the corpora cardiaca of the major families of all three suborders of the Odonata were identified by one or more of the following methods: (1) Isolation of the peptides from a methanolic extract of the corpora cardiaca by liquid chromatography, peak monitoring by fluorescence of the Trp residue and comparison of the retention time with those of known synthetic peptides of Odonata. (2) Hyperlipaemic bioassays of the HPLC-generated fractions either in Locusta migratoria or, in a few cases, in Anax imperator or Orthetrum julia. (3) Sequencing of the isolated, bioactive HPLAC fraction by Edman degradation. (4) Mass spectrometric measurement of the isolated, bioactive fraction. Sequence assignment revealed that the investigated Odonata species always contain only one adipokinetic peptide. This is always an octapeptide. The suborder Zygoptera contains the peptide code-named Psein-AKH, the Anisozygoptera and the families Aeshnidae, Cordulegastridae and Macromiidae of the Anisoptera contain Anaim-AKH, whereas Gomphidae, Corduliidae (with the exception of Syncordulia gracilis) and Libellulidae contain Libau-AKH; one species of Libellulidae has Erysi-AKH, a very conservative modification of Libau-AKH (one point mutation). When these structural data are interpreted in conjunction with existing phylogenies of Odonata, they support the following: (1) Zygoptera are monophyletic and not paraphyletic. (2) Anisozygoptera and Anisoptera are sister groups and contain the ancestral Anaim-AKH which is independently and convergently mutated to Libau-AKH in Gomphidae and Libellulidae. (3) The Corduliidae are of special interest. Only Corduliidae sensu stricto appear to contain Libau-AKH, other species placed into this family by most authorities contain the ancestral Anaim-AKH. Possibly, assignments of AKHs can untangle the paraphyly of this family.

  9. Redescription and phylogenetic position of Myxobolus aeglefini and Myxobolus platessae n. comb. (Myxosporea), parasites in the cartilage of some North Atlantic marine fishes, with notes on the phylogeny and classification of the Platysporina.

    PubMed

    Karlsbakk, Egil; Kristmundsson, Árni; Albano, Marco; Brown, Paul; Freeman, Mark A

    2017-02-01

    Myxobolus 'aeglefini' Auerbach, 1906 was originally described from cranial cartilage of North sea haddock (Melanogrammus aeglefinus), but has subsequently been recorded from cartilaginous tissues of a range of other gadoid hosts, from pleuronectids and from lumpsucker (Cyclopterus lumpus) in the North Atlantic and from a zoarcid fish in the Japan Sea (Pacific). We obtained partial small-subunit rDNA sequences of Myxobolus 'aeglefini' from gadoids and pleuronectids from Norway and Iceland. The sequences from gadoids and pleuronectids represented two different genotypes, showing 98.2% identity. Morphometric studies on the spores from selected gadids and pleuronectids revealed slight but statistically significant differences in spore dimensions associated with the genotypes, the spores from pleuronectids were thicker and with larger polar capsules. We identify the morpho- and genotype from gadoids with Myxobolus 'aeglefini' sensu Auerbach, and the one from pleuronectids with Sphaerospora platessae Woodcock, 1904 as Myxobolus platessae n. comb. The latter species was originally described from Irish Sea plaice (Pleuronectes platessa). Myxobolus albi Picon et al., 2009 described from the common goby Pomatoschistus microps in Scotland is a synonym of M. 'aeglefini'. The Pacific Myxobolus 'aeglefini' represents a separate species, showing only 97.4-97.6% identity to the Atlantic species. In phylogenetic analyses based on SSU rDNA sequences, these and some related marine chondrotropic Myxobolus spp. form a distinct well supported group. This clusters with freshwater and marine myxobolids and Triangula and Cardimyxobolus species, in a basal clade in the phylogeny of the Platysporina. Members of family Myxobilatidae, Ortholinea spp. (currently Ortholineidae) and sequences of some other urinary system infecting myxosporeans form a well supported clade among members of the suborder Platysporina. Based on phylogenetic analyses, we propose the following changes to the

  10. Mitochondrial function in Antarctic nototheniids with ND6 translocation.

    PubMed

    Mark, Felix C; Lucassen, Magnus; Strobel, Anneli; Barrera-Oro, Esteban; Koschnick, Nils; Zane, Lorenzo; Patarnello, Tomaso; Pörtner, Hans O; Papetti, Chiara

    2012-01-01

    Fish of the suborder Notothenioidei have successfully radiated into the Southern Ocean and today comprise the dominant fish sub-order in Antarctic waters in terms of biomass and species abundance. During evolution in the cold and stable Antarctic climate, the Antarctic lineage of notothenioids developed several unique physiological adaptations, which make them extremely vulnerable to the rapid warming of Antarctic waters currently observed. Only recently, a further phenomenon exclusive to notothenioid fish was reported: the translocation of the mitochondrial gene encoding the NADH Dehydrogenase subunit 6 (ND6), an indispensable part of complex I in the mitochondrial electron transport system.This study investigated the potential physiological consequences of ND6 translocation for the function and thermal sensitivity of the electron transport system in isolated liver mitochondria of the two nototheniid species Notothenia coriiceps and Notothenia rossii, with special attention to the contributions of complex I (NADH DH) and complex II (Succinate DH) to oxidative phosphorylation. Furthermore, enzymatic activities of NADH:Cytochrome c Oxidoreductase and Cytochrome C Oxidase were measured in membrane-enriched tissue extracts.During acute thermal challenge (0-15°C), capacities of mitochondrial respiration and enzymatic function in the liver could only be increased until 9°C. Mitochondrial complex I (NADH Dehydrogenase) was fully functional but displayed a higher thermal sensitivity than the other complexes of the electron transport system, which may specifically result from its unique amino acid composition, revealing a lower degree of stability in notothenioids in general. We interpret the translocation of ND6 as functionally neutral but the change in amino acid sequence as adaptive and supportive of cold stenothermy in Antarctic nototheniids. From these findings, an enhanced sensitivity to ocean warming can be deduced for Antarctic notothenioid fish.

  11. Bacterial communities from shoreline environments (costa da morte, northwestern Spain) affected by the prestige oil spill.

    PubMed

    Alonso-Gutiérrez, Jorge; Figueras, Antonio; Albaigés, Joan; Jiménez, Núria; Viñas, Marc; Solanas, Anna M; Novoa, Beatriz

    2009-06-01

    The bacterial communities in two different shoreline matrices, rocks and sand, from the Costa da Morte, northwestern Spain, were investigated 12 months after being affected by the Prestige oil spill. Culture-based and culture-independent approaches were used to compare the bacterial diversity present in these environments with that at a nonoiled site. A long-term effect of fuel on the microbial communities in the oiled sand and rock was suggested by the higher proportion of alkane and polyaromatic hydrocarbon (PAH) degraders and the differences in denaturing gradient gel electrophoresis patterns compared with those of the reference site. Members of the classes Alphaproteobacteria and Actinobacteria were the prevailing groups of bacteria detected in both matrices, although the sand bacterial community exhibited higher species richness than the rock bacterial community did. Culture-dependent and -independent approaches suggested that the genus Rhodococcus could play a key role in the in situ degradation of the alkane fraction of the Prestige fuel together with other members of the suborder Corynebacterineae. Moreover, other members of this suborder, such as Mycobacterium spp., together with Sphingomonadaceae bacteria (mainly Lutibacterium anuloederans), were related as well to the degradation of the aromatic fraction of the Prestige fuel. The multiapproach methodology applied in the present study allowed us to assess the complexity of autochthonous microbial communities related to the degradation of heavy fuel from the Prestige and to isolate some of their components for a further physiological study. Since several Corynebacterineae members related to the degradation of alkanes and PAHs were frequently detected in this and other supralittoral environments affected by the Prestige oil spill along the northwestern Spanish coast, the addition of mycolic acids to bioremediation amendments is proposed to favor the presence of these degraders in long-term fuel pollution

  12. Revision of the Massarineae (Pleosporales, Dothideomycetes)

    PubMed Central

    Tanaka, K.; Hirayama, K.; Yonezawa, H.; Sato, G.; Toriyabe, A.; Kudo, H.; Hashimoto, A.; Matsumura, M.; Harada, Y.; Kurihara, Y.; Shirouzu, T.; Hosoya, T.

    2015-01-01

    We here taxonomically revise the suborder Massarineae (Pleosporales, Dothideomycetes, Ascomycota). Sequences of SSU and LSU nrDNA and the translation elongation factor 1-alpha gene (tef1) are newly obtained from 106 Massarineae taxa that are phylogenetically analysed along with published sequences of 131 taxa in this suborder retrieved from GenBank. We recognise 12 families and five unknown lineages in the Massarineae. Among the nine families previously known, the monophyletic status of the Dictyosporiaceae, Didymosphaeriaceae, Latoruaceae, Macrodiplodiopsidaceae, Massarinaceae, Morosphaeriaceae, and Trematosphaeriaceae was strongly supported with bootstrap support values above 96 %, while the clades of the Bambusicolaceae and the Lentitheciaceae are moderately supported. Two new families, Parabambusicolaceae and Sulcatisporaceae, are proposed. The Parabambusicolaceae is erected to accommodate Aquastroma and Parabambusicola genera nova, as well as two unnamed Monodictys species. The Parabambusicolaceae is characterised by depressed globose to hemispherical ascomata with or without surrounding stromatic tissue, and multi-septate, clavate to fusiform, hyaline ascospores. The Sulcatisporaceae is established for Magnicamarosporium and Sulcatispora genera nova and Neobambusicola. The Sulcatisporaceae is characterised by subglobose ascomata with a short ostiolar neck, trabeculate pseudoparaphyses, clavate asci, broadly fusiform ascospores, and ellipsoid to subglobose conidia with or without striate ornamentation. The genus Periconia and its relatives are segregated from the Massarinaceae and placed in a resurrected family, the Periconiaceae. We have summarised the morphological and ecological features, and clarified the accepted members of each family. Ten new genera, 22 new species, and seven new combinations are described and illustrated. The complete ITS sequences of nrDNA are also provided for all new taxa for use as barcode markers. PMID:26955201

  13. Small, Smaller, Smallest: The Origins and Evolution of Ancient Dual Symbioses in a Phloem-Feeding Insect

    PubMed Central

    Bennett, Gordon M.; Moran, Nancy A.

    2013-01-01

    Many insects rely on bacterial symbionts with tiny genomes specialized for provisioning nutrients lacking in host diets. Xylem sap and phloem sap are both deficient as insect diets, but differ dramatically in nutrient content, potentially affecting symbiont genome evolution. For sap-feeding insects, sequenced symbiont genomes are available only for phloem-feeding examples from the suborder Sternorrhyncha and xylem-feeding examples from the suborder Auchenorrhyncha, confounding comparisons. We sequenced genomes of the obligate symbionts, Sulcia muelleri and Nasuia deltocephalinicola, of the phloem-feeding pest insect, Macrosteles quadrilineatus (Auchenorrhyncha: Cicadellidae). Our results reveal that Nasuia-ALF has the smallest bacterial genome yet sequenced (112 kb), and that the Sulcia-ALF genome (190 kb) is smaller than that of Sulcia in other insect lineages. Together, these symbionts retain the capability to synthesize the 10 essential amino acids, as observed for several symbiont pairs from xylem-feeding Auchenorrhyncha. Nasuia retains genes enabling synthesis of two amino acids, DNA replication, transcription, and translation. Both symbionts have lost genes underlying ATP synthesis through oxidative phosphorylation, possibly as a consequence of the enriched sugar content of phloem. Shared genomic features, including reassignment of the UGA codon from Stop to tryptophan, and phylogenetic results suggest that Nasuia-ALF is most closely related to Zinderia, the betaproteobacterial symbiont of spittlebugs. Thus, Nasuia/Zinderia and Sulcia likely represent ancient associates that have co-resided in hosts since the divergence of leafhoppers and spittlebugs >200 Ma, and possibly since the origin of the Auchenorrhyncha, >260 Ma. PMID:23918810

  14. The evolution of bat vestibular systems in the face of potential antagonistic selection pressures for flight and echolocation.

    PubMed

    Davies, Kalina T J; Bates, Paul J J; Maryanto, Ibnu; Cotton, James A; Rossiter, Stephen J

    2013-01-01

    The vestibular system maintains the body's sense of balance and, therefore, was probably subject to strong selection during evolutionary transitions in locomotion. Among mammals, bats possess unique traits that place unusual demands on their vestibular systems. First, bats are capable of powered flight, which in birds is associated with enlarged semicircular canals. Second, many bats have enlarged cochleae associated with echolocation, and both cochleae and semicircular canals share a space within the petrosal bone. To determine how bat vestibular systems have evolved in the face of these pressures, we used micro-CT scans to compare canal morphology across species with contrasting flight and echolocation capabilities. We found no increase in canal radius in bats associated with the acquisition of powered flight, but canal radius did correlate with body mass in bat species from the suborder Yangochiroptera, and also in non-echolocating Old World fruit bats from the suborder Yinpterochiroptera. No such trend was seen in members of the Yinpterochiroptera that use laryngeal echolocation, although canal radius was associated with wing-tip roundedness in this group. We also found that the vestibular system scaled with cochlea size, although the relationship differed in species that use constant frequency echolocation. Across all bats, the shape of the anterior and lateral canals was associated with large cochlea size and small body size respectively, suggesting differential spatial constraints on each canal depending on its orientation within the skull. Thus in many echolocating bats, it seems that the combination of small body size and enlarged cochlea together act as a principal force on the vestibular system. The two main groups of echolocating bats displayed different canal morphologies, in terms of size and shape in relation to body mass and cochlear size, thus suggesting independent evolutionary pathways and offering tentative support for multiple acquisitions of

  15. Bacterial Communities from Shoreline Environments (Costa da Morte, Northwestern Spain) Affected by the Prestige Oil Spill▿ †

    PubMed Central

    Alonso-Gutiérrez, Jorge; Figueras, Antonio; Albaigés, Joan; Jiménez, Núria; Viñas, Marc; Solanas, Anna M.; Novoa, Beatriz

    2009-01-01

    The bacterial communities in two different shoreline matrices, rocks and sand, from the Costa da Morte, northwestern Spain, were investigated 12 months after being affected by the Prestige oil spill. Culture-based and culture-independent approaches were used to compare the bacterial diversity present in these environments with that at a nonoiled site. A long-term effect of fuel on the microbial communities in the oiled sand and rock was suggested by the higher proportion of alkane and polyaromatic hydrocarbon (PAH) degraders and the differences in denaturing gradient gel electrophoresis patterns compared with those of the reference site. Members of the classes Alphaproteobacteria and Actinobacteria were the prevailing groups of bacteria detected in both matrices, although the sand bacterial community exhibited higher species richness than the rock bacterial community did. Culture-dependent and -independent approaches suggested that the genus Rhodococcus could play a key role in the in situ degradation of the alkane fraction of the Prestige fuel together with other members of the suborder Corynebacterineae. Moreover, other members of this suborder, such as Mycobacterium spp., together with Sphingomonadaceae bacteria (mainly Lutibacterium anuloederans), were related as well to the degradation of the aromatic fraction of the Prestige fuel. The multiapproach methodology applied in the present study allowed us to assess the complexity of autochthonous microbial communities related to the degradation of heavy fuel from the Prestige and to isolate some of their components for a further physiological study. Since several Corynebacterineae members related to the degradation of alkanes and PAHs were frequently detected in this and other supralittoral environments affected by the Prestige oil spill along the northwestern Spanish coast, the addition of mycolic acids to bioremediation amendments is proposed to favor the presence of these degraders in long-term fuel pollution

  16. The Evolution of Bat Vestibular Systems in the Face of Potential Antagonistic Selection Pressures for Flight and Echolocation

    PubMed Central

    Davies, Kalina T. J.; Bates, Paul J. J.; Maryanto, Ibnu; Cotton, James A.; Rossiter, Stephen J.

    2013-01-01

    The vestibular system maintains the body’s sense of balance and, therefore, was probably subject to strong selection during evolutionary transitions in locomotion. Among mammals, bats possess unique traits that place unusual demands on their vestibular systems. First, bats are capable of powered flight, which in birds is associated with enlarged semicircular canals. Second, many bats have enlarged cochleae associated with echolocation, and both cochleae and semicircular canals share a space within the petrosal bone. To determine how bat vestibular systems have evolved in the face of these pressures, we used micro-CT scans to compare canal morphology across species with contrasting flight and echolocation capabilities. We found no increase in canal radius in bats associated with the acquisition of powered flight, but canal radius did correlate with body mass in bat species from the suborder Yangochiroptera, and also in non-echolocating Old World fruit bats from the suborder Yinpterochiroptera. No such trend was seen in members of the Yinpterochiroptera that use laryngeal echolocation, although canal radius was associated with wing-tip roundedness in this group. We also found that the vestibular system scaled with cochlea size, although the relationship differed in species that use constant frequency echolocation. Across all bats, the shape of the anterior and lateral canals was associated with large cochlea size and small body size respectively, suggesting differential spatial constraints on each canal depending on its orientation within the skull. Thus in many echolocating bats, it seems that the combination of small body size and enlarged cochlea together act as a principal force on the vestibular system. The two main groups of echolocating bats displayed different canal morphologies, in terms of size and shape in relation to body mass and cochlear size, thus suggesting independent evolutionary pathways and offering tentative support for multiple acquisitions of

  17. The Complete Mitochondrial Genome of Meloidogyne graminicola (Tylenchina): A Unique Gene Arrangement and Its Phylogenetic Implications

    PubMed Central

    Sun, Longhua; Zhuo, Kan; Lin, Borong; Wang, Honghong; Liao, Jinling

    2014-01-01

    Meloidogyne graminicola is one of the most economically important plant parasitic-nematodes (PPNs). In the present study, we determined the complete mitochondrial (mt) DNA genome sequence of this plant pathogen. Compared with other PPNs genera, this genome (19,589 bp) is only slightly smaller than that of Pratylenchus vulnus (21,656 bp). The nucleotide composition of the whole mtDNA sequence of M. graminicola is significantly biased toward A and T, with T being the most favored nucleotide and C being the least favored. The A+T content of the entire genome is 83.51%. The mt genome of M. graminicola contains 36 genes (lacking atp8) that are transcribed in the same direction. The gene arrangement of the mt genome of M. graminicola is unique. A total of 21 out of 22 tRNAs possess a DHU loop only, while tRNASer(AGN) lacks a DHU loop. The two large noncoding regions (2,031 bp and 5,063 bp) are disrupted by tRNASer(UCN). Phylogenetic analysis based on concatenated amino acid sequences of 12 protein-coding genes support the monophylies of the three orders Rhabditida, Mermithida and Trichinellida, the suborder Rhabditina and the three infraorders Spiruromorpha, Oxyuridomorpha and Ascaridomorpha, but do not support the monophylies of the two suborders Spirurina and Tylenchina, and the three infraorders Rhabditomorpha, Panagrolaimomorpha and Tylenchomorpha. The four Tylenchomorpha species including M. graminicola, P. vulnus, H. glycines and R. similis from the superfamily Tylenchoidea are placed within a well-supported monophyletic clade, but far from the other two Tylenchomorpha species B. xylophilus and B. mucronatus of Aphelenchoidea. In the clade of Tylenchoidea, M. graminicola is sister to P. vulnus, and H. glycines is sister to R. similis, which suggests root-knot nematodes has a closer relationship to Pratylenchidae nematodes than to cyst nematodes. PMID:24892428

  18. Mitochondrial Function in Antarctic Nototheniids with ND6 Translocation

    PubMed Central

    Mark, Felix C.; Lucassen, Magnus; Strobel, Anneli; Barrera-Oro, Esteban; Koschnick, Nils; Zane, Lorenzo; Patarnello, Tomaso; Pörtner, Hans O.; Papetti, Chiara

    2012-01-01

    Fish of the suborder Notothenioidei have successfully radiated into the Southern Ocean and today comprise the dominant fish sub-order in Antarctic waters in terms of biomass and species abundance. During evolution in the cold and stable Antarctic climate, the Antarctic lineage of notothenioids developed several unique physiological adaptations, which make them extremely vulnerable to the rapid warming of Antarctic waters currently observed. Only recently, a further phenomenon exclusive to notothenioid fish was reported: the translocation of the mitochondrial gene encoding the NADH Dehydrogenase subunit 6 (ND6), an indispensable part of complex I in the mitochondrial electron transport system. This study investigated the potential physiological consequences of ND6 translocation for the function and thermal sensitivity of the electron transport system in isolated liver mitochondria of the two nototheniid species Notothenia coriiceps and Notothenia rossii, with special attention to the contributions of complex I (NADH DH) and complex II (Succinate DH) to oxidative phosphorylation. Furthermore, enzymatic activities of NADH∶Cytochrome c Oxidoreductase and Cytochrome C Oxidase were measured in membrane-enriched tissue extracts. During acute thermal challenge (0–15°C), capacities of mitochondrial respiration and enzymatic function in the liver could only be increased until 9°C. Mitochondrial complex I (NADH Dehydrogenase) was fully functional but displayed a higher thermal sensitivity than the other complexes of the electron transport system, which may specifically result from its unique amino acid composition, revealing a lower degree of stability in notothenioids in general. We interpret the translocation of ND6 as functionally neutral but the change in amino acid sequence as adaptive and supportive of cold stenothermy in Antarctic nototheniids. From these findings, an enhanced sensitivity to ocean warming can be deduced for Antarctic notothenioid fish. PMID

  19. Widespread atypical mitochondrial DNA structure in isopods (Crustacea, Peracarida) related to a constitutive heteroplasmy in terrestrial species.

    PubMed

    Doublet, Vincent; Raimond, Roland; Grandjean, Frédéric; Lafitte, Alexandra; Souty-Grosset, Catherine; Marcadé, Isabelle

    2012-03-01

    Metazoan mitochondrial DNA (mtDNA) is generally composed of circular monomeric molecules. However, a few exceptions do exist and among them two terrestrial isopods Armadillidium vulgare and Porcellionides pruinosus have an atypical mtDNA composed of linear monomers associated with circular "head-to-head" dimers: a very unusual structure for animal mtDNA genome. To assess the distribution of this atypical mtDNA among isopods, we performed RFLP and Southern blot analyses on mtDNA of 16 terrestrial (Oniscidea family) and two aquatic isopod species: the marine Sphaeroma serratum (suborder Flabellifera, sister group of Oniscidea) and the freshwater Asellus aquaticus (Asellota, early derived taxon of isopod). The atypical mtDNA structure was observed in 15 terrestrial isopod species and A. aquaticus, suggesting a wide distribution of atypical mtDNA among isopods. However, a typical metazoan mtDNA structure was detected in the marine isopod S. serratum and the Oniscidea Ligia oceanica . Our results suggest two possible scenarios: an early origin of the atypical mtDNA in isopods followed by reversion to the typical ancestral mtDNA structure for several species, or a convergent appearance of the atypical mtDNA structure in two isopod suborders. We compare this distribution of the atypical mtDNA structure with the presence of a heteroplasmy also observed in the mtDNA of several terrestrial isopod species. We discuss if this transmitted heteroplasmy is vectored by the atypical mtDNA and its impact on the maintenance of the atypical mtDNA in isopods.

  20. Molecular Characterization of Poxviruses Associated with Tattoo Skin Lesions in UK Cetaceans

    PubMed Central

    Blacklaws, Barbara A.; Gajda, Anna M.; Tippelt, Sabine; Jepson, Paul D.; Deaville, Rob; Van Bressem, Marie-Francoise; Pearce, Gareth P.

    2013-01-01

    There is increasing concern for the well-being of cetacean populations around the UK. Tattoo skin disease (characterised by irregular, grey, black or yellowish, stippled cutaneous lesions) caused by poxvirus infection is a potential health indicatora potential health indicator for cetaceans. Limited sequence data indicates that cetacean poxviruses (CPVs) belong to an unassigned genus of the Chordopoxvirinae. To obtain further insight into the phylogenetic relationships between CPV and other Chordopoxvirinae members we partially characterized viral DNA originating from tattoo lesions collected in Delphinidae and Phocoenidae stranded along the UK coastline in 1998–2008. We also evaluated the presence of CPV in skin lesions other than tattoos to examine specificity and sensitivity of visual diagnosis. After DNA extraction, regions of the DNA polymerase and DNA topoisomerase I genes were amplified by PCR, sequenced and compared with other isolates. The presence of CPV DNA was demonstrated in tattoos from one striped dolphin (Stenella coeruleoalba), eight harbour porpoises (Phocoena phocoena) and one short-beaked common dolphin (Delphinus delphis) and in one ‘dubious tattoo’ lesion detected in one other porpoise. Seventeen of the 18 PCR positive skin lesions had been visually identified as tattoos and one as a dubious tattoo. None of the other skin lesions were PCR positive. Thus, visual identification had a 94.4% sensitivity and 100% specificity. The DNA polymerase PCR was most effective in detecting CPV DNA. Limited sequence phylogeny grouped the UK samples within the odontocete poxviruses (CPV group 1) and indicated that two different poxvirus lineages infect the Phocoenidae and the Delphinidae. The phylogenetic tree had three major branches: one with the UK Phocoenidae viruses, one with the Delphinidae isolates and one for the mysticete poxvirus (CPV group 2). This implies a radiation of poxviruses according to the host suborder and the families within these

  1. Purification and characterization of insulin and the C-peptide of proinsulin from Przewalski's horse, zebra, rhino, and tapir (Perissodactyla).

    PubMed

    Henry, J S; Lance, V A; Conlon, J M

    1993-02-01

    Within the order Perissodactyla, the primary structure of insulin has been strongly conserved. Insulin from Przewalski's horse and the mountain zebra (suborder Hippomorpha) is the same as that from the domestic horse and differs from insulin from the white rhinoceros and mountain tapir (suborder Ceratomorpha) by a single substitution (Gly-->Ser) at position 9 in the A-chain. A second molecular form of Przewalski's horse insulin isolated in this study was shown to represent the gamma-ethyl ester of the Glu17 residue of the A-chain. This component was probably formed during the extraction of the pancreas with acidified ethanol. The amino acid sequence of the C-peptide of proinsulin has been less well conserved. Zebra C-peptide comprises 31 amino acid residues and differs from Przewalski's horse and domestic horse C-peptide by one substitution (Gln30-->Pro). Rhino C-peptide was isolated only in a truncated form corresponding to residues (1-23) of intact C-peptide. Its amino acid sequence contains three substitutions compared with the corresponding region of horse C-peptide. It is postulated that the substitution (Pro23-->Thr) renders rhino C-peptide more liable to proteolytic cleavage by a chymotrypsin-like enzyme than horse C-peptide. C-peptide could not be identified in the extract of tapir pancreas, suggesting that proteolytic degradation may have been more extensive than in the rhino. In contrast to the ox and pig (order Artiodactyla), there was no evidence for the expression of more than one proinsulin gene in the species of Perissodactyla examined.

  2. Intrachromosomal rearrangements in two representatives of the genus Saltator (Thraupidae, Passeriformes) and the occurrence of heteromorphic Z chromosomes.

    PubMed

    dos Santos, Michelly da Silva; Kretschmer, Rafael; Silva, Fabio Augusto Oliveira; Ledesma, Mario Angel; O'Brien, Patricia C M; Ferguson-Smith, Malcolm A; Del Valle Garnero, Analía; de Oliveira, Edivaldo Herculano Corrêa; Gunski, Ricardo José

    2015-10-01

    Saltator is a genus within family Thraupidae, the second largest family of Passeriformes, with more than 370 species found exclusively in the New World. Despite this, only a few species have had their karyotypes analyzed, most of them only with conventional staining. The diploid number is close to 80, and chromosome morphology is similar to the usual avian karyotype. Recent studies using cross-species chromosome painting have shown that, although the chromosomal morphology and number are similar to many species of birds, Passeriformes exhibit a complex pattern of paracentric and pericentric inversions in the chromosome homologous to GGA1q in two different suborders, Oscines and Suboscines. Hence, considering the importance and species richness of Thraupidae, this study aims to analyze two species of genus Saltator, the golden-billed saltator (S. aurantiirostris) and the green-winged saltator (S. similis) by means of classical cytogenetics and cross-species chromosome painting using Gallus gallus and Leucopternis albicollis probes, and also 5S and 18S rDNA and telomeric sequences. The results show that the karyotypes of these species are similar to other species of Passeriformes. Interestingly, the Z chromosome appears heteromorphic in S. similis, varying in morphology from acrocentric to metacentric. 5S and 18S probes hybridize to one pair of microchromosomes each, and telomeric sequences produce signals only in the terminal regions of chromosomes. FISH results are very similar to the Passeriformes already analyzed by means of molecular cytogenetics (Turdus species and Elaenia spectabilis). However, the paracentric and pericentric inversions observed in Saltator are different from those detected in these species, an observation that helps to explain the probable sequence of rearrangements. As these rearrangements are found in both suborders of Passeriformes (Oscines and Suboscines), we propose that the fission of GGA1 and inversions in GGA1q have occurred very

  3. Contrasting patterns of adaptive sequence convergence among echolocating mammals.

    PubMed

    Lambert, Matthew J; Nevue, Alexander A; Portfors, Christine V

    2017-03-20

    Several recent studies have described genes demonstrating adaptive sequence convergence between echolocating bats and dolphin, suggesting that common selective pressures can induce common molecular changes, even in distantly related species. However, in the case of the auditory genes Otoferlin (Otof), Cadherin 23 (Cdh23) and Protocadherin 15 (Pcdh15), the reported sequence convergence was supported only by incongruent gene and species trees and counts of convergent substitutions. Therefore, it remains unclear whether echolocating bats and dolphin really do demonstrate evidence of adaptive sequence convergence, or whether there is simply a high level of random background convergence in these genes. To address this question, we estimated the number of convergent and divergent amino acid substitutions along all independent branches of a sufficiently deep phylogeny containing between 22 and 32 mammals for each gene, and compared convergence between the two proposed suborders of bat, Yangochiroptera and Yinpterochiroptera, and dolphin. We find no support for convergence between bats and dolphin in the gene Pcdh15. For the gene Otof we report minimal evidence for convergent evolution only between the Yinpterochiroptera and dolphin. Cdh23 displayed a high level of convergence between dolphin and the Yinpterochiroptera. In addition, dolphin and certain members of the Yangochiroptera that emit high frequency echolocation calls shared several unique convergent substitutions. These results indicate that the convergent evolution of Cdh23 was likely driven by selection for hearing above a certain frequency threshold. Moreover, the contrasting patterns of convergence between the two bat suborders and dolphin in all auditory genes studied thus far suggest echolocation may have evolved independently in the Yinpterochiroptera and Yangochiroptera.

  4. Family-Level Sampling of Mitochondrial Genomes in Coleoptera: Compositional Heterogeneity and Phylogenetics.

    PubMed

    Timmermans, Martijn J T N; Barton, Christopher; Haran, Julien; Ahrens, Dirk; Culverwell, C Lorna; Ollikainen, Alison; Dodsworth, Steven; Foster, Peter G; Bocak, Ladislav; Vogler, Alfried P

    2015-12-08

    Mitochondrial genomes are readily sequenced with recent technology and thus evolutionary lineages can be densely sampled. This permits better phylogenetic estimates and assessment of potential biases resulting from heterogeneity in nucleotide composition and rate of change. We gathered 245 mitochondrial sequences for the Coleoptera representing all 4 suborders, 15 superfamilies of Polyphaga, and altogether 97 families, including 159 newly sequenced full or partial mitogenomes. Compositional heterogeneity greatly affected 3rd codon positions, and to a lesser extent the 1st and 2nd positions, even after RY coding. Heterogeneity also affected the encoded protein sequence, in particular in the nad2, nad4, nad5, and nad6 genes. Credible tree topologies were obtained with the nhPhyML ("nonhomogeneous") algorithm implementing a model for branch-specific equilibrium frequencies. Likelihood searches using RAxML were improved by data partitioning by gene and codon position. Finally, the PhyloBayes software, which allows different substitution processes for amino acid replacement at various sites, produced a tree that best matched known higher level taxa and defined basal relationships in Coleoptera. After rooting with Neuropterida outgroups, suborder relationships were resolved as (Polyphaga (Myxophaga (Archostemata + Adephaga))). The infraorder relationships in Polyphaga were (Scirtiformia (Elateriformia ((Staphyliniformia + Scarabaeiformia) (Bostrichiformia (Cucujiformia))))). Polyphagan superfamilies were recovered as monophyla except Staphylinoidea (paraphyletic for Scarabaeiformia) and Cucujoidea, which can no longer be considered a valid taxon. The study shows that, although compositional heterogeneity is not universal, it cannot be eliminated for some mitochondrial genes, but dense taxon sampling and the use of appropriate Bayesian analyses can still produce robust phylogenetic trees.

  5. Genomes of Ashbya Fungi Isolated from Insects Reveal Four Mating-Type Loci, Numerous Translocations, Lack of Transposons, and Distinct Gene Duplications

    PubMed Central

    Dietrich, Fred S.; Voegeli, Sylvia; Kuo, Sidney; Philippsen, Peter

    2013-01-01

    The filamentous fungus Ashbya gossypii is a cotton pathogen transmitted by insects. It is readily grown and manipulated in the laboratory and is commercially exploited as a natural overproducer of vitamin B2. Our previous genome analysis of A. gossypii isolate ATCC10895, collected in Trinidad nearly 100 years ago, revealed extensive synteny with the Saccharomyces cerevisiae genome, leading us to use it as a model organism to understand the evolution of filamentous growth. To further develop Ashbya as a model system, we have investigated the ecological niche of A. gossypii and isolated additional strains and a sibling species, both useful in comparative analysis. We isolated fungi morphologically similar to A. gossypii from different plant-feeding insects of the suborder Heteroptera, generated a phylogenetic tree based on rDNA-ITS sequences, and performed high coverage short read sequencing with one A. gossypii isolate from Florida, a new species, Ashbya aceri, isolated in North Carolina, and a genetically marked derivative of ATCC10895 intensively used for functional studies. In contrast to S. cerevisiae, all strains carry four not three mating type loci, adding a new puzzle in the evolution of Ashbya species. Another surprise was the genome identity of 99.9% between the Florida strain and ATCC10895, isolated in Trinidad. The A. aceri and A. gossypii genomes show conserved gene orders rearranged by eight translocations, 90% overall sequence identity, and fewer tandem duplications in the A. aceri genome. Both species lack transposable elements. Finally, our work identifies plant-feeding insects of the suborder Heteroptera as the most likely natural reservoir of Ashbya, and that infection of cotton and other plants may be incidental to the growth of the fungus in its insect host. PMID:23749448

  6. Family-Level Sampling of Mitochondrial Genomes in Coleoptera: Compositional Heterogeneity and Phylogenetics

    PubMed Central

    Timmermans, Martijn J. T. N.; Barton, Christopher; Haran, Julien; Ahrens, Dirk; Culverwell, C. Lorna; Ollikainen, Alison; Dodsworth, Steven; Foster, Peter G.; Bocak, Ladislav; Vogler, Alfried P.

    2016-01-01

    Mitochondrial genomes are readily sequenced with recent technology and thus evolutionary lineages can be densely sampled. This permits better phylogenetic estimates and assessment of potential biases resulting from heterogeneity in nucleotide composition and rate of change. We gathered 245 mitochondrial sequences for the Coleoptera representing all 4 suborders, 15 superfamilies of Polyphaga, and altogether 97 families, including 159 newly sequenced full or partial mitogenomes. Compositional heterogeneity greatly affected 3rd codon positions, and to a lesser extent the 1st and 2nd positions, even after RY coding. Heterogeneity also affected the encoded protein sequence, in particular in the nad2, nad4, nad5, and nad6 genes. Credible tree topologies were obtained with the nhPhyML (“nonhomogeneous”) algorithm implementing a model for branch-specific equilibrium frequencies. Likelihood searches using RAxML were improved by data partitioning by gene and codon position. Finally, the PhyloBayes software, which allows different substitution processes for amino acid replacement at various sites, produced a tree that best matched known higher level taxa and defined basal relationships in Coleoptera. After rooting with Neuropterida outgroups, suborder relationships were resolved as (Polyphaga (Myxophaga (Archostemata + Adephaga))). The infraorder relationships in Polyphaga were (Scirtiformia (Elateriformia ((Staphyliniformia + Scarabaeiformia) (Bostrichiformia (Cucujiformia))))). Polyphagan superfamilies were recovered as monophyla except Staphylinoidea (paraphyletic for Scarabaeiformia) and Cucujoidea, which can no longer be considered a valid taxon. The study shows that, although compositional heterogeneity is not universal, it cannot be eliminated for some mitochondrial genes, but dense taxon sampling and the use of appropriate Bayesian analyses can still produce robust phylogenetic trees. PMID:26645679

  7. A revised dated phylogeny of the arachnid order Opiliones.

    PubMed

    Sharma, Prashant P; Giribet, Gonzalo

    2014-01-01

    Dating the Opiliones tree of life has become an important enterprise for this group of arthropods, due to their ancient origins and important biogeographic implications. To incorporate both methodological innovations in molecular dating as well as new systematic discoveries of harvestman diversity, we conducted total evidence dating on a data set uniting morphological and/or molecular sequence data for 47 Opiliones species, including all four well-known Palaeozoic fossils, to test the placement of both fossils and newly discovered lineages in a single analysis. Furthermore, we investigated node dating with a phylogenomic data set of 24,202 amino acid sites for 14 species of Opiliones, sampling all extant suborders. In this way, we approached molecular dating of basal harvestman phylogeny using different data sets and approaches to assess congruence of divergence time estimates. In spite of the markedly different composition of data sets, our results show congruence across all analyses for age estimates of basal nodes that are well constrained with respect to fossil calibrations (e.g., Opiliones, Palpatores). By contrast, derived nodes that lack fossil calibrations (e.g., the suborders Cyphophthalmi, and Laniatores) have large uncertainty intervals in diversification times, particularly in the total evidence dating analysis, reflecting the dearth of calibration points and undersampling of derived lineages. Total evidence dating consistently produced older median ages than node dating for ingroup nodes, due to the nested placement of multiple Palaeozoic fossils. Our analyses support basal diversification of Opiliones in the Ordovician-Devonian period, corroborating the inferred ancient origins of this arthropod order, and underscore the importance of diversity discovery-both paleontological and neontological-in evolutionary inference.

  8. When the body hides the ancestry: phylogeny of morphologically modified epizoic earwigs based on molecular evidence.

    PubMed

    Kocarek, Petr; John, Vaclav; Hulva, Pavel

    2013-01-01

    Here, we present a study regarding the phylogenetic positions of two enigmatic earwig lineages whose unique phenotypic traits evolved in connection with ectoparasitic relationships with mammals. Extant earwigs (Dermaptera) have traditionally been divided into three suborders: the Hemimerina, Arixeniina, and Forficulina. While the Forficulina are typical, well-known, free-living earwigs, the Hemimerina and Arixeniina are unusual epizoic groups living on molossid bats (Arixeniina) or murid rodents (Hemimerina). The monophyly of both epizoic lineages is well established, but their relationship to the remainder of the Dermaptera is controversial because of their extremely modified morphology with paedomorphic features. We present phylogenetic analyses that include molecular data (18S and 28S ribosomal DNA and histone-3) for both Arixeniina and Hemimerina for the first time. This data set enabled us to apply a rigorous cladistics approach and to test competing hypotheses that were previously scattered in the literature. Our results demonstrate that Arixeniidae and Hemimeridae belong in the dermapteran suborder Neodermaptera, infraorder Epidermaptera, and superfamily Forficuloidea. The results support the sister group relationships of Arixeniidae+Chelisochidae and Hemimeridae+Forficulidae. This study demonstrates the potential for rapid and substantial macroevolutionary changes at the morphological level as related to adaptive evolution, in this case linked to the utilization of a novel trophic niche based on an epizoic life strategy. Our results also indicate that the evolutionary consequences of the transition to an ectoparazitic mode of living, which is extremely rare in earwigs, have biased previous morphology-based hypotheses regarding the phylogeny of this insect group.

  9. Phylogenetic and geographic patterns of bartonella host shifts among bat species.

    PubMed

    McKee, Clifton D; Hayman, David T S; Kosoy, Michael Y; Webb, Colleen T

    2016-10-01

    The influence of factors contributing to parasite diversity in individual hosts and communities are increasingly studied, but there has been less focus on the dominant processes leading to parasite diversification. Using bartonella infections in bats as a model system, we explored the influence of three processes that can contribute to bartonella diversification and lineage formation: (1) spatial correlation in the invasion and transmission of bartonella among bats (phylogeography); (2) divergent adaptation of bartonellae to bat hosts and arthropod vectors; and (3) evolutionary codivergence between bats and bartonellae. Using a combination of global fit techniques and ancestral state reconstruction, we found that codivergence appears to be the dominant process leading to diversification of bartonella in bats, with lineages of bartonellae corresponding to separate bat suborders, superfamilies, and families. Furthermore, we estimated the rates at which bartonellae shift bat hosts across taxonomic scales (suborders, superfamilies, and families) and found that transition rates decrease with increasing taxonomic distance, providing support for a mechanism that can contribute to the observed evolutionary congruence between bats and their associated bartonellae. While bartonella diversification is associated with host sympatry, the influence of this factor is minor compared to the influence of codivergence and there is a clear indication that some bartonella lineages span multiple regions, particularly between Africa and Southeast Asia. Divergent adaptation of bartonellae to bat hosts and arthropod vectors is apparent and can dilute the overall pattern of codivergence, however its importance in the formation of Bartonella lineages in bats is small relative to codivergence. We argue that exploring all three of these processes yields a more complete understanding of bat-bartonella relationships and the evolution of the genus Bartonella, generally. Application of these

  10. Novel marine actinobacteria from emerald Andaman & Nicobar Islands: a prospective source for industrial and pharmaceutical byproducts

    PubMed Central

    2013-01-01

    Background Andaman and Nicobar Islands situated in the eastern part of Bay of Bengal are one of the distinguished biodiversity hotspot. Even though number of studies carried out on the marine flora and fauna, the studies on actinobacteria from Andaman and Nicobar Islands are meager. The aim of the present study was to screen the actinobacteria for their characterization and identify the potential sources for industrial and pharmaceutical byproducts. Results A total of 26 actinobacterial strains were isolated from the marine sediments collected from various sites of Port Blair Bay where no collection has been characterized previously. Isolates were categorized under the genera: Saccharopolyspora, Streptomyces, Nocardiopsis, Streptoverticillium, Microtetraspora, Actinopolyspora, Actinokineospora and Dactylosporangium. Majority of the isolates were found to produce industrially important enzymes such as amylase, protease, gelatinase, lipase, DNase, cellulase, urease and phosphatase, and also exhibited substantial antibacterial activity against human pathogens. 77% of isolates exhibited significant hemolytic activity. Among 26 isolates, three strains (NIOT-VKKMA02, NIOT-VKKMA22 and NIOT-VKKMA26) were found to generate appreciable extent of surfactant, amylase, cellulase and protease enzyme. NIOT-VKKMA02 produced surfactant using kerosene as carbon source and emulsified upto E24–63.6%. Moreover, NIOT-VKKMA02, NIOT-VKKMA22 and NIOT-VKKMA26 synthesized 13.27 U/ml, 9.85 U/ml and 8.03 U/ml amylase; 7.75 U/ml, 5.01 U/ml and 2.08 U/ml of cellulase and 11.34 U/ml, 6.89 U/ml and 3.51 U/ml of protease enzyme, respectively. Conclusions High diversity of marine actinobacteria was isolated and characterized in this work including undescribed species and species not previously reported from emerald Andaman and Nicobar Islands, including Streptomyces griseus, Streptomyces venezuelae and Saccharopolyspora salina. The enhanced salt, pH and temperature tolerance of the actinobacterial

  11. Co-evolution of RNA polymerase with RbpA in the phylum Actinobacteria

    PubMed Central

    Dey, Abhinav; Adithi, V.R.; Chatterji, Dipankar

    2012-01-01

    The role of RbpA in the backdrop of M. smegmatis showed that it rescues mycobacterial RNA polymerase from rifampicin-mediated inhibition (Dey et al., 2010; Dey et al., 2011). Paget and co-workers (Paget et al., 2001; Newell et al., 2006) have revealed that RbpA homologs occur exclusively in actinobacteria. Newell et al. (2006) showed that MtbRbpA, when complemented in a ∆rbpA mutant of S. coelicolor, showed a low recovery of MIC (from 0.75 to 2 μg/ml) as compared to complementation by native RbpA of S. coelicolor (MIC increases from 0.75 to 11 μg/ml). Our studies on MsRbpA show that it is a differential marker for M. smegmatis RNA polymerase as compared to E. coli RNA polymerase at IC50 levels of rifampicin. A recent sequence-based analysis by Lane and Darst (2010) has shown that RNA polymerases from Proteobacteria and Actinobacteria have had a divergent evolution. E. coli is a representative of Proteobacteria and M. smegmatis is an Actinobacterium. RbpA has an exclusive occurrence in Actinobacteria. Since protein–protein interactions might not be conserved across different species, therefore, the probable reason for the indifference of MsRbpA toward E. coli RNA polymerase could be the lineage-specific differences between actinobacterial and proteobacterial RNA polymerases. These observations led us to ask the question as to whether the evolution of RbpA in Actinobacteria followed the same route as that of RNA polymerase subunits from actinobacterial species. We show that the exclusivity of RbpA in Actinobacteria and the unique evolution of RNA polymerase in this phylum share a co-evolutionary link. We have addressed this issue by a blending of experimental and bioinformatics based approaches. They comprise of induction of bacterial cultures coupled to rifampicin-tolerance, transcription assays and statistical comparison of phylogenetic trees for different pairs of proteins in actinobacteria. PMID:27896048

  12. Next-generation systematics: An innovative approach to resolve the structure of complex prokaryotic taxa

    NASA Astrophysics Data System (ADS)

    Sangal, Vartul; Goodfellow, Michael; Jones, Amanda L.; Schwalbe, Edward C.; Blom, Jochen; Hoskisson, Paul A.; Sutcliffe, Iain C.

    2016-12-01

    Prokaryotic systematics provides the fundamental framework for microbiological research but remains a discipline that relies on a labour- and time-intensive polyphasic taxonomic approach, including DNA-DNA hybridization, variation in 16S rRNA gene sequence and phenotypic characteristics. These techniques suffer from poor resolution in distinguishing between closely related species and often result in misclassification and misidentification of strains. Moreover, guidelines are unclear for the delineation of bacterial genera. Here, we have applied an innovative phylogenetic and taxogenomic approach to a heterogeneous actinobacterial taxon, Rhodococcus, to identify boundaries for intrageneric and supraspecific classification. Seven species-groups were identified within the genus Rhodococcus that are as distantly related to one another as they are to representatives of other mycolic acid containing actinobacteria and can thus be equated with the rank of genus. It was also evident that strains assigned to rhodococcal species-groups are underspeciated with many misclassified using conventional taxonomic criteria. The phylogenetic and taxogenomic methods used in this study provide data of theoretical value for the circumscription of generic and species boundaries and are also of practical significance as they provide a robust basis for the classification and identification of rhodococci of agricultural, industrial and medical/veterinary significance.

  13. Diversity and dynamics of free-living and particle-associated Betaproteobacteria and Actinobacteria in relation to phytoplankton and zooplankton communities.

    PubMed

    Parveen, Bushra; Reveilliez, Jean-Philippe; Mary, Isabelle; Ravet, Viviane; Bronner, Gisèle; Mangot, Jean-François; Domaizon, Isabelle; Debroas, Didier

    2011-09-01

    The diversity of attached and free-living Actinobacteria and Betaproteobacteria, based on 16S rRNA gene sequences, was investigated in a mesotrophic lake during two periods of contrasting phytoplankton dominance. Comparison analyses showed a phylogenetic difference between attached and free-living communities for the two bacterial groups. For Betaproteobacteria, the betaI clade was detected at all sampling dates in free-living and attached bacterial communities and was the dominant clade contributing to 57.8% of the total retrieved operational taxonomic units (OTUs). For Actinobacteria, the acIV cluster was found to be dominant, followed by acI contributing to 45% and 25% of the total retrieved OTUs, respectively. This study allows the determination of eight new putative clades among the Betaproteobacteria termed lbI-lbVIII and a new putative clade named acLBI belonging to the Actinobacteria. The seasonal dynamics of phytoplankton and zooplankton communities have been reflected as changes in distinct bacterial phylotypes for both attached and free-living communities. For attached communities, relationships were observed between Actinobacteria and Chrysophyceae, and between Betaproteobacteria and Dinophyceae and Chlorophyceae biomass. On the other hand, within free-living communities, few actinobacterial clades were found to be dependent on either nutrients or phytoplankton communities, whereas Betaproteobacteria were mainly associated with biological parameters (i.e. phytoplankton and copepod communities).

  14. Triacylglycerol accumulation and oxidative stress in Rhodococcus species: differential effects of pro-oxidants on lipid metabolism.

    PubMed

    Urbano, Susana Bequer; Di Capua, Cecilia; Cortez, Néstor; Farías, María E; Alvarez, Héctor M

    2014-03-01

    In general, members of Rhodococcus genus are highly resistant to desiccation. Desiccation is a complex process which includes the formation of reactive oxygen species that results in significant damage to cells. In this study, we demonstrate that extremophile actinobacterial strains isolated from diverse environments, mainly belonging to Rhodococcus genus, exhibited high tolerance to the pro-oxidants hydrogen peroxide (H2O2) and methyl viologen (MV). In addition, we investigated the possible interconnections between the responses of the oleaginous Rhodococcus opacus PD630 to oxidative stress and lipid metabolism, since both processes demand a metabolic reorganization of cells. Experiments with metabolic inhibitors showed differential effects of both pro-oxidants on lipid metabolism in PD630 cells. The inhibition of carotenoid biosynthesis by the addition of diphenylamine to the media negatively affected the tolerance of cells to H2O2, but not to MV. The inhibition of triacylglycerol (TAG) biosynthesis and accumulation in PD630 did not affect the tolerance of cells to H2O2 and MV; whereas, the blockage of lipolysis decreased the tolerance of cells to H2O2 (but not MV) under carbon-starvation conditions. Interestingly, the addition of MV to the media (but not H2O2) induced a reduction of TAG accumulation by cells. Resuming, results of this study revealed metabolic connections between lipid metabolism and oxidative stress responses in R. opacus PD630, and probably in other extremophile TAG-accumulating rhodococci.

  15. Variable genetic architectures produce virtually identical molecules in bacterial symbionts of fungus-growing ants

    PubMed Central

    Sit, Clarissa S.; Ruzzini, Antonio C.; Van Arnam, Ethan B.; Ramadhar, Timothy R.; Currie, Cameron R.; Clardy, Jon

    2015-01-01

    Small molecules produced by Actinobacteria have played a prominent role in both drug discovery and organic chemistry. As part of a larger study of the actinobacterial symbionts of fungus-growing ants, we discovered a small family of three previously unreported piperazic acid-containing cyclic depsipeptides, gerumycins A–C. The gerumycins are slightly smaller versions of dentigerumycin, a cyclic depsipeptide that selectively inhibits a common fungal pathogen, Escovopsis. We had previously identified this molecule from a Pseudonocardia associated with Apterostigma dentigerum, and now we report the molecule from an associate of the more highly derived ant Trachymyrmex cornetzi. The three previously unidentified compounds, gerumycins A–C, have essentially identical structures and were produced by two different symbiotic Pseudonocardia spp. from ants in the genus Apterostigma found in both Panama and Costa Rica. To understand the similarities and differences in the biosynthetic pathways that produced these closely related molecules, the genomes of the three producing Pseudonocardia were sequenced and the biosynthetic gene clusters identified. This analysis revealed that dramatically different biosynthetic architectures, including genomic islands, a plasmid, and the use of spatially separated genetic loci, can lead to molecules with virtually identical core structures. A plausible evolutionary model that unifies these disparate architectures is presented. PMID:26438860

  16. Effects of plant genotype and growth stage on the structure of bacterial communities associated with potato (Solanum tuberosum L.).

    PubMed

    van Overbeek, Leo; van Elsas, Jan Dirk

    2008-05-01

    The effects of genotype, plant growth and experimental factors (soil and year) on potato-associated bacterial communities were studied. Cultivars Achirana Inta, Désirée, Merkur and transgenic Désirée line DL12 (containing T4 lysozyme gene) were assessed in two field experiments. Cross-comparisons between both experiments were made using Désirée plants. Culture-dependent and -independent approaches were used to demonstrate effects on total bacterial, actinobacterial and Pseudomonas communities in bulk and rhizosphere soils and endospheres. PCR-denaturing gradient gel electrophoresis fingerprints prepared with group-specific primers were analyzed using multivariate analyses and revealed that bacterial communities in Achirana Inta plants differed most from those of Désirée and Merkur. No significant effects were found between Désirée and DL12 lines. Plant growth stage strongly affected different plant-associated communities in both experiments. To investigate the effect of plant-associated communities on plant health, 800 isolates from rhizospheres and endospheres at the flowering stage were tested for suppression of Ralstonia solanacearum biovar 2 and/or Rhizoctonia solani AG3. A group of isolates closely resembling Lysobacter sp. dominated in young plants. Its prevalence was affected by plant growth stage and experiment rather than by plant genotype. It was concluded that plant growth stage overwhelmed any effect of plant genotype on the bacterial communities associated with potato.

  17. Gancidin W, a potential low-toxicity antimalarial agent isolated from an endophytic Streptomyces SUK10.

    PubMed

    Zin, Noraziah Mohamad; Baba, Mohd Shukri; Zainal-Abidin, Abu Hassan; Latip, Jalifah; Mazlan, Noor Wini; Edrada-Ebel, RuAngelie

    2017-01-01

    Endophytic Streptomyces strains are potential sources for novel bioactive molecules. In this study, the diketopiperazine gancidin W (GW) was isolated from the endophytic actinobacterial genus Streptomyces, SUK10, obtained from the bark of Shorea ovalis tree, and it was tested in vivo against Plasmodium berghei PZZ1/100. GW exhibited an inhibition rate of nearly 80% at 6.25 and 3.125 μg kg(-1) body weight on day four using the 4-day suppression test method on male ICR strain mice. Comparing GW at both concentrations with quinine hydrochloride and normal saline as positive and negative controls, respectively, 50% of the mice treated with 3.125 μg kg(-1) body weight managed to survive for more than 11 months after infection, which almost reached the life span of normal mice. Biochemical tests of selected enzymes and proteins in blood samples of mice treated with GW were also within normal levels; in addition, no abnormalities or injuries were found on internal vital organs. These findings indicated that this isolated bioactive compound from Streptomyces SUK10 exhibits very low toxicity and is a good candidate for potential use as an antimalarial agent in an animal model.

  18. Environmental factors shaping the abundance and distribution of laccase-encoding bacterial community with potential phenolic oxidase capacity during composting.

    PubMed

    Lu, Lunhui; Zeng, Guangming; Fan, Changzheng; Guo, Jinsong; Zhang, Jiachao; Chen, Ming; Wu, Haipeng; Yuan, Yujie; He, Xiaoxiao; He, Yan

    2015-11-01

    Increasing molecular evidence points to a wide occurrence of laccase-like multicopper oxidase (LMCO)-encoding genes in bacteria. Most researches mainly focused on the bacterial LMCO diversity, whereas the processes and the environmental factors responsible for structuring bacterial LMCO communities remain relatively unknown in a composting system. Six gene libraries were constructed from samples in representative stages during composting. A total of 185 sequences obtained from sample DNA extracts were classified to 59 operational taxonomic units (OTUs) based on 10 % cutoff. The distribution profile of bacterial LMCO genes showed that proteobacterial- and actinobacterial-associated species were the dominant communities during composting. Pearson correlation analysis indicated that the pile temperature and water-soluble carbon (WSC) content were significantly positively correlated with bacterial LMCO gene OTU numbers, Chao1 and Shannon index, whereas the humic acid (HA)-like carbon content had the most significant effect on the distribution of the bacterial LMCO genes during composting by redundancy analysis. These findings will improve the understanding of the mutual relationship between environmental factors and bacterial LMCO community compositions in composting.

  19. Microbial Communities and Chemosynthesis in Yellowstone Lake Sublacustrine Hydrothermal Vent Waters

    PubMed Central

    Yang, Tingting; Lyons, Shawn; Aguilar, Carmen; Cuhel, Russell; Teske, Andreas

    2011-01-01

    Five sublacustrine thermal spring locations from 1 to 109 m water depth in Yellowstone Lake were surveyed by 16S ribosomal RNA gene sequencing in relation to their chemical composition and dark CO2 fixation rates. They harbor distinct chemosynthetic bacterial communities, depending on temperature (16–110°C) and electron donor supply (H2S <1 to >100 μM; NH3 <0.5 to >10 μM). Members of the Aquificales, most closely affiliated with the genus Sulfurihydrogenibium, are the most frequently recovered bacterial 16S rRNA gene phylotypes in the hottest samples; the detection of these thermophilic sulfur-oxidizing autotrophs coincided with maximal dark CO2 fixation rates reaching near 9 μM C h−1 at temperatures of 50–60°C. Vents at lower temperatures yielded mostly phylotypes related to the mesophilic gammaproteobacterial sulfur oxidizer Thiovirga. In contrast, cool vent water with low chemosynthetic activity yielded predominantly phylotypes related to freshwater Actinobacterial clusters with a cosmopolitan distribution. PMID:21716640

  20. Unique microbial signatures of the alien Hawaiian marine sponge Suberites zeteki.

    PubMed

    Zhu, Ping; Li, Quanzi; Wang, Guangyi

    2008-04-01

    Invasive species poses a threat to the world's oceans. Alien sponges account for the majority of introduced marine species in the isolated Hawaiian reef ecosystems. In this study, cultivation-dependent and cultivation-independent techniques were applied to investigate microbial consortia associated with the alien Hawaiian marine sponge Suberites zeteki. Its microbial communities were diverse with representatives of Actinobacteria, Firmicutes, alpha- and gamma-Proteobacteria, Bacteroidetes, Chlamydiae, Planctomycetes, and Cyanobacteria. Specifically, the genus Chlamydia was identified for the first time from marine sponges, and two genera (Streptomyces and Rhodococcus) were added to the short list of culturable actinobacteria from sponges. Culturable microbial communities were dominated by Bacillus species (63%) and contained actinobacterial species closely affiliated with those from habitats other than marine sponges. Cyanobacterial clones were clustered with free-living cyanobacteria from water column and other environmental samples; they show no affiliation with other sponge-derived cyanobacteria. The low sequence similarity of Planctomycetes, Chlamydiae, and alpha-Proteobacteria clones to other previously described sequences suggested that S. zeteki may contain new lineages of these bacterial groups. The microbial diversity of S. zeteki was different from that of other studied marine sponges. This is the first report on microbial communities of alien marine invertebrate species. For the first time, it provides an insight into microbial structure within alien marine sponges in the Hawaiian marine ecosystems.

  1. Next-generation systematics: An innovative approach to resolve the structure of complex prokaryotic taxa

    PubMed Central

    Sangal, Vartul; Goodfellow, Michael; Jones, Amanda L.; Schwalbe, Edward C.; Blom, Jochen; Hoskisson, Paul A.; Sutcliffe, Iain C.

    2016-01-01

    Prokaryotic systematics provides the fundamental framework for microbiological research but remains a discipline that relies on a labour- and time-intensive polyphasic taxonomic approach, including DNA-DNA hybridization, variation in 16S rRNA gene sequence and phenotypic characteristics. These techniques suffer from poor resolution in distinguishing between closely related species and often result in misclassification and misidentification of strains. Moreover, guidelines are unclear for the delineation of bacterial genera. Here, we have applied an innovative phylogenetic and taxogenomic approach to a heterogeneous actinobacterial taxon, Rhodococcus, to identify boundaries for intrageneric and supraspecific classification. Seven species-groups were identified within the genus Rhodococcus that are as distantly related to one another as they are to representatives of other mycolic acid containing actinobacteria and can thus be equated with the rank of genus. It was also evident that strains assigned to rhodococcal species-groups are underspeciated with many misclassified using conventional taxonomic criteria. The phylogenetic and taxogenomic methods used in this study provide data of theoretical value for the circumscription of generic and species boundaries and are also of practical significance as they provide a robust basis for the classification and identification of rhodococci of agricultural, industrial and medical/veterinary significance. PMID:27924912

  2. Prospects of using marine actinobacteria as probiotics in aquaculture.

    PubMed

    Das, Surajit; Ward, Louise R; Burke, Chris

    2008-12-01

    Chemotherapeutic agents have been banned for disease management in aquaculture systems due to the emergence of antibiotic resistance gene and enduring residual effects in the environments. Instead, microbial interventions in sustainable aquaculture have been proposed, and among them, the most popular and practical approach is the use of probiotics. A range of microorganisms have been used so far as probiotics, which include Gram-negative and Gram-positive bacteria, yeast, bacteriophages, and unicellular algae. The results are satisfactory and promising; however, to combat the latest infectious diseases, the search for a new strain for probiotics is essential. Marine actinobacteria were designated as the chemical factory a long time ago, and quite a large number of chemical substances have been isolated to date. The potent actinobacterial genera are Streptomyces; Micromonospora; and a novel, recently described genus, Salinispora. Despite the existence of all the significant features of a good probiont, actinobacteria have been hardly used as probiotics in aquaculture. However, this group of bacteria promises to supply the most potential probiotic strains in the future.

  3. Remarkable impact of PAHs and TPHs on the richness and diversity of bacterial species in surface soils exposed to long-term hydrocarbon pollution.

    PubMed

    Benedek, Tibor; Vajna, Balázs; Táncsics, András; Márialigeti, Károly; Lányi, Szabolcs; Máthé, István

    2013-11-01

    Nowadays, because of substantial use of petroleum-derived fuels the number and extension of hydrocarbon polluted terrestrial ecosystems is in growth worldwide. In remediation of aforementioned sites bioremediation still tends to be an innovative, environmentally attractive technology. Although huge amount of information is available concerning the hydrocarbon degradation potential of cultivable hydrocarbonoclastic bacteria little is known about the in situ long-term effects of petroleum derived compounds on the structure of soil microbiota. Therefore, in this study our aim was to determine the long-term impact of total petroleum hydrocarbons (TPHs), volatile petroleum hydrocarbons (VPHs), total alkyl benzenes (TABs) as well as of polycyclic aromatic hydrocarbons (PAHs) on the structure of bacterial communities of four different contaminated soil samples. Our results indicated that a very high amount of TPH affected positively the diversity of hydrocarbonoclastic bacteria. This finding was supported by the occurrence of representatives of the α-, β-, γ-Proteobacteria, Actinobacteria, Flavobacteriia and Bacilli classes. High concentration of VPHs and TABs contributed to the predominance of actinobacterial isolates. In PAH impacted samples the concentration of PAHs negatively correlated with the diversity of bacterial species. Heavily PAH polluted soil samples were mainly inhabited by the representatives of the β-, γ-Proteobacteria (overwhelming dominance of Pseudomonas sp.) and Actinobacteria.

  4. Phylogenetic analyses of phylum Actinobacteria based on whole genome sequences.

    PubMed

    Verma, Mansi; Lal, Devi; Kaur, Jaspreet; Saxena, Anjali; Kaur, Jasvinder; Anand, Shailly; Lal, Rup

    2013-09-01

    Actinobacteria constitute one of the largest and ancient taxonomic phylum within the domain bacteria and are well known for their secondary metabolites. Considerable variation in the metabolic properties, genome size and GC content of the members of this phylum has been observed. Therefore, the placement of new or existing species based on 16S rRNA gene sometimes becomes problematic due to the low congruence level. In the present study, phylogeny of ninety actinobacterial genomes was reconstructed using single gene and whole genome based data. Where alignment-free phylogenetic method was found to be more robust, the concatenation of 94 proteins improved the resolution which all single gene based phylogenies failed to resolve. The comprehensive analysis of 94 conserved proteins resulted in a total of 42,447 informative sites, which is so far the largest meta-alignment obtained for this phylum. But the ultimate resolved phylogeny was obtained by generating a consensus tree by combining the information from single gene and genome based phylogenies. The present investigation clearly revealed that the consensus approach is a useful tool for phylogenetic inference and the taxonomic affiliations must be based on this approach. The consensus approach suggested that there is a need for taxonomic amendments of the orders Frankiales and Micrococcales.

  5. Detection of biosynthetic gene and phytohormone production by endophytic actinobacteria associated with Solanum lycopersicum and their plant-growth-promoting effect.

    PubMed

    Passari, Ajit Kumar; Chandra, Preeti; Zothanpuia; Mishra, Vineet Kumar; Leo, Vincent Vineeth; Gupta, Vijai Kumar; Kumar, Brijesh; Singh, Bhim Pratap

    2016-10-01

    In the present study, fifteen endophytic actinobacterial isolates recovered from Solanum lycopersicum were studied for their antagonistic potential and plant-growth-promoting (PGP) traits. Among them, eight isolates showed significant antagonistic and PGP traits, identified by amplification of the 16S rRNA gene. Isolate number DBT204, identified as Streptomyces sp., showed multiple PGP traits tested in planta and improved a range of growth parameters in seedlings of chili (Capsicum annuum L.) and tomato (S. lycopersicum L.). Further, genes of indole acetic acid (iaaM) and 1-aminocyclopropane-1-carboxylate (ACC) deaminase (acdS) were successively amplified from five strains. Six antibiotics (trimethoprim, fluconazole, chloramphenicol, nalidixic acid, rifampicin and streptomycin) and two phytohormones [indole acetic acid (IAA) and kinetin (KI)] were detected and quantified in Streptomyces sp. strain DBT204 using UPLC-ESI-MS/MS. The study indicates the potential of these PGP strains for production of phytohormones and shows the presence of biosynthetic genes responsible for production of secondary metabolites. It is the first report showing production of phytohormones (IAA and KI) by endophytic actinobacteria having PGP and biosynthetic potential. We propose Streptomyces sp. strain DBT204 for inoculums production and development of biofertilizers for enhancing growth of chili and tomato seedlings.

  6. Phylogenetic diversity and biological activity of actinobacteria isolated from the Chukchi Shelf marine sediments in the Arctic Ocean.

    PubMed

    Yuan, Meng; Yu, Yong; Li, Hui-Rong; Dong, Ning; Zhang, Xiao-Hua

    2014-03-06

    Marine environments are a rich source of Actinobacteria and have the potential to produce a wide variety of biologically active secondary metabolites. In this study, we used four selective isolation media to culture Actinobacteria from the sediments collected from the Chukchi Shelf in the Arctic Ocean. A total of 73 actinobacterial strains were isolated. Based on repetitive DNA fingerprinting analysis, we selected 30 representatives for partial characterization according to their phylogenetic diversity, antimicrobial activities and secondary-metabolite biosynthesis genes. Results from the 16S rRNA gene sequence analysis indicated that the 30 strains could be sorted into 18 phylotypes belonging to 14 different genera: Agrococcus, Arsenicicoccus, Arthrobacter, Brevibacterium, Citricoccus, Janibacter, Kocuria, Microbacterium, Microlunatus, Nocardioides, Nocardiopsis, Saccharopolyspora, Salinibacterium and Streptomyces. To our knowledge, this paper is the first report on the isolation of Microlunatus genus members from marine habitats. Of the 30 isolates, 11 strains exhibited antibacterial and/or antifungal activity, seven of which have activities against Bacillus subtilis and Candida albicans. All 30 strains have at least two biosynthetic genes, one-third of which possess more than four biosynthetic genes. This study demonstrates the significant diversity of Actinobacteria in the Chukchi Shelf sediment and their potential for producing biologically active compounds and novel material for genetic manipulation or combinatorial biosynthesis.

  7. Protease inhibitors from marine actinobacteria as a potential source for antimalarial compound.

    PubMed

    Karthik, L; Kumar, Gaurav; Keswani, Tarun; Bhattacharyya, Arindam; Chandar, S Sarath; Bhaskara Rao, K V

    2014-01-01

    The study was planned to screen the marine actinobacterial extract for the protease inhibitor activity and its anti- Pf activity under in vitro and in vivo conditions. Out of 100 isolates, only 3 isolates exhibited moderate to high protease inhibitor activities on trypsin, chymotrypsin and proteinase K. Based on protease inhibitor activity 3 isolates were chosen for further studies. The potential isolate was characterized by polyphasic approach and identified as Streptomyces sp LK3 (JF710608). The lead compound was identified as peptide from Streptomyces sp LK3. The double-reciprocal plot displayed inhibition mode is non-competitive and it confirms the irreversible nature of protease inhibitor. The peptide from Streptomyces sp LK3 extract showed significant anti plasmodial activity (IC50: 25.78 µg/ml). In in vivo model, the highest level of parasitemia suppression (≈ 45%) was observed in 600 mg/kg of the peptide. These analyses revealed no significant changes were observed in the spleen and liver tissue during 8 dpi. The results confirmed up-regulation of TGF-β and down regulation of TNF-α in tissue and serum level in PbA infected peptide treated mice compared to PbA infection. The results obtained infer that the peptide possesses anti- Pf activity activity. It suggests that the extracts have novel metabolites and could be considered as a potential source for drug development.

  8. Comprehensive investigation of marine Actinobacteria associated with the sponge Halichondria panicea.

    PubMed

    Schneemann, Imke; Nagel, Kerstin; Kajahn, Inga; Labes, Antje; Wiese, Jutta; Imhoff, Johannes F

    2010-06-01

    Representatives of Actinobacteria were isolated from the marine sponge Halichondria panicea collected from the Baltic Sea (Germany). For the first time, a comprehensive investigation was performed with regard to phylogenetic strain identification, secondary metabolite profiling, bioactivity determination, and genetic exploration of biosynthetic genes, especially concerning the relationships of the abundance of biosynthesis gene fragments to the number and diversity of produced secondary metabolites. All strains were phylogenetically identified by 16S rRNA gene sequence analyses and were found to belong to the genera Actinoalloteichus, Micrococcus, Micromonospora, Nocardiopsis, and Streptomyces. Secondary metabolite profiles of 46 actinobacterial strains were evaluated, 122 different substances were identified, and 88 so far unidentified compounds were detected. The extracts from most of the cultures showed biological activities. In addition, the presence of biosynthesis genes encoding polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) in 30 strains was established. It was shown that strains in which either PKS or NRPS genes were identified produced a significantly higher number of metabolites and exhibited a larger number of unidentified, possibly new metabolites than other strains. Therefore, the presence of PKS and NRPS genes is a good indicator for the selection of strains to isolate new natural products.

  9. Complete genome sequence of Jiangella gansuensis strain YIM 002(T) (DSM 44835(T)), the type species of the genus Jiangella and source of new antibiotic compounds.

    PubMed

    Jiao, Jian-Yu; Carro, Lorena; Liu, Lan; Gao, Xiao-Yang; Zhang, Xiao-Tong; Hozzein, Wael N; Lapidus, Alla; Huntemann, Marcel; Reddy, T B K; Varghese, Neha; Hadjithomas, Michalis; Ivanova, Natalia N; Göker, Markus; Pillay, Manoj; Eisen, Jonathan A; Woyke, Tanja; Klenk, Hans-Peter; Kyrpides, Nikos C; Li, Wen-Jun

    2017-01-01

    Jiangella gansuensis strain YIM 002(T) is the type strain of the type species of the genus Jiangella, which is at the present time composed of five species, and was isolated from desert soil sample in Gansu Province (China). The five strains of this genus are clustered in a monophyletic group when closer actinobacterial genera are used to infer a 16S rRNA gene sequence phylogeny. The study of this genome is part of the GenomicEncyclopedia ofBacteria andArchaea project, and here we describe the complete genome sequence and annotation of this taxon. The genome of J. gansuensis strain YIM 002(T) contains a single scaffold of size 5,585,780 bp, which involves 149 pseudogenes, 4905 protein-coding genes and 50 RNA genes, including 2520 hypothetical proteins and 4 rRNA genes. From the investigation of genome sizes of Jiangella species, J. gansuensis shows a smaller size, which indicates this strain might have discarded too much genetic information to adapt to desert environment. Seven new compounds from this bacterium have recently been described; however, its potential should be higher, as secondary metabolite gene cluster analysis predicted 60 gene clusters, including the potential to produce the pristinamycin.

  10. A Survey of Nucleotide Cyclases in Actinobacteria: Unique Domain Organization and Expansion of the Class III Cyclase Family in Mycobacterium tuberculosis

    PubMed Central

    Sivakumar, K.; Krupa, A.; Srinivasan, N.

    2004-01-01

    Cyclic nucleotides are well-known second messengers involved in the regulation of important metabolic pathways or virulence factors. There are six different classes of nucleotide cyclases that can accomplish the task of generating cAMP, and four of these are restricted to the prokaryotes. The role of cAMP has been implicated in the virulence and regulation of secondary metabolites in the phylum Actinobacteria, which contains important pathogens, such as Mycobacterium tuberculosis, M. leprae, M. bovis and Corynebacterium, and industrial organisms from the genus Streptomyces. We have analysed the actinobacterial genome sequences found in current databases for the presence of different classes of nucleotide cyclases, and find that only class III cyclases are present in these organisms. Importantly, prominent members such as M. tuberculosis and M. leprae have 17 and 4 class III cyclases, respectively, encoded in their genomes, some of which display interesting domain fusions seen for the first time. In addition, a pseudogene corresponding to a cyclase from M. avium has been identified as the only cyclase pseudogene in M. tuberculosis and M. bovis. The Corynebacterium and Streptomyces genomes encode only a single adenylyl cyclase each, both of which have corresponding orthologues in M. tuberculosis. A clustering of the cyclase domains in Actinobacteria reveals the presence of typical eukaryote-like, fungi-like and other bacteria-like class III cyclase sequences within this phylum, suggesting that these proteins may have significant roles to play in this important group of organisms. PMID:18629044

  11. Phylogenetic Diversity and Biological Activity of Actinobacteria Isolated from the Chukchi Shelf Marine Sediments in the Arctic Ocean

    PubMed Central

    Yuan, Meng; Yu, Yong; Li, Hui-Rong; Dong, Ning; Zhang, Xiao-Hua

    2014-01-01

    Marine environments are a rich source of Actinobacteria and have the potential to produce a wide variety of biologically active secondary metabolites. In this study, we used four selective isolation media to culture Actinobacteria from the sediments collected from the Chukchi Shelf in the Arctic Ocean. A total of 73 actinobacterial strains were isolated. Based on repetitive DNA fingerprinting analysis, we selected 30 representatives for partial characterization according to their phylogenetic diversity, antimicrobial activities and secondary-metabolite biosynthesis genes. Results from the 16S rRNA gene sequence analysis indicated that the 30 strains could be sorted into 18 phylotypes belonging to 14 different genera: Agrococcus, Arsenicicoccus, Arthrobacter, Brevibacterium, Citricoccus, Janibacter, Kocuria, Microbacterium, Microlunatus, Nocardioides, Nocardiopsis, Saccharopolyspora, Salinibacterium and Streptomyces. To our knowledge, this paper is the first report on the isolation of Microlunatus genus members from marine habitats. Of the 30 isolates, 11 strains exhibited antibacterial and/or antifungal activity, seven of which have activities against Bacillus subtilis and Candida albicans. All 30 strains have at least two biosynthetic genes, one-third of which possess more than four biosynthetic genes. This study demonstrates the significant diversity of Actinobacteria in the Chukchi Shelf sediment and their potential for producing biologically active compounds and novel material for genetic manipulation or combinatorial biosynthesis. PMID:24663116

  12. Comprehensive Investigation of Marine Actinobacteria Associated with the Sponge Halichondria panicea▿ †

    PubMed Central

    Schneemann, Imke; Nagel, Kerstin; Kajahn, Inga; Labes, Antje; Wiese, Jutta; Imhoff, Johannes F.

    2010-01-01

    Representatives of Actinobacteria were isolated from the marine sponge Halichondria panicea collected from the Baltic Sea (Germany). For the first time, a comprehensive investigation was performed with regard to phylogenetic strain identification, secondary metabolite profiling, bioactivity determination, and genetic exploration of biosynthetic genes, especially concerning the relationships of the abundance of biosynthesis gene fragments to the number and diversity of produced secondary metabolites. All strains were phylogenetically identified by 16S rRNA gene sequence analyses and were found to belong to the genera Actinoalloteichus, Micrococcus, Micromonospora, Nocardiopsis, and Streptomyces. Secondary metabolite profiles of 46 actinobacterial strains were evaluated, 122 different substances were identified, and 88 so far unidentified compounds were detected. The extracts from most of the cultures showed biological activities. In addition, the presence of biosynthesis genes encoding polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) in 30 strains was established. It was shown that strains in which either PKS or NRPS genes were identified produced a significantly higher number of metabolites and exhibited a larger number of unidentified, possibly new metabolites than other strains. Therefore, the presence of PKS and NRPS genes is a good indicator for the selection of strains to isolate new natural products. PMID:20382810

  13. In-vitro antimicrobial activity of marine actinobacteria against multidrug resistance Staphylococcus aureus

    PubMed Central

    Sathish, Kumar SR; Kokati, Venkata Bhaskara Rao

    2012-01-01

    Objective To investigate the antibacterial activity of marine actinobacteria against multidrug resistance Staphylococcus aureus (MDRSA). Methods Fifty one actinobacterial strains were isolated from salt pans soil, costal area in Kothapattanam, Ongole, Andhra Pradesh. Primary screening was done using cross-streak method against MDRSA. The bioactive compounds are extracted from efficient actinobacteria using solvent extraction. The antimicrobial activity of crude and solvent extracts was performed using Kirby-Bauer method. MIC for ethyl acetate extract was determined by modified agar well diffusion method. The potent actinobacteria are identified using Nonomura key, Shirling and Gottlieb 1966 with Bergey's manual of determinative bacteriology. Results Among the fifty one isolates screened for antibacterial activity, SRB25 were found efficient against MDRSA. The ethyl acetate extracts showed high inhibition against test organism. MIC test was performed with the ethyl acetate extract against MDRSA and found to be 1 000 µg/mL. The isolated actinobacteria are identified as Streptomyces sp with the help of Nonomura key. Conclusions The current investigation reveals that the marine actinobacteria from salt pan environment can be able to produce new drug molecules against drug resistant microorganisms. PMID:23569848

  14. Ketide Synthase (KS) Domain Prediction and Analysis of Iterative Type II PKS Gene in Marine Sponge-Associated Actinobacteria Producing Biosurfactants and Antimicrobial Agents.

    PubMed

    Selvin, Joseph; Sathiyanarayanan, Ganesan; Lipton, Anuj N; Al-Dhabi, Naif Abdullah; Valan Arasu, Mariadhas; Kiran, George S

    2016-01-01

    The important biological macromolecules, such as lipopeptide and glycolipid biosurfactant producing marine actinobacteria were analyzed and their potential linkage between type II polyketide synthase (PKS) genes was explored. A unique feature of type II PKS genes is their high amino acid (AA) sequence homology and conserved gene organization. These enzymes mediate the biosynthesis of polyketide natural products with enormous structural complexity and chemical nature by combinatorial use of various domains. Therefore, deciphering the order of AA sequence encoded by PKS domains tailored the chemical structure of polyketide analogs still remains a great challenge. The present work deals with an in vitro and in silico analysis of PKS type II genes from five actinobacterial species to correlate KS domain architecture and structural features. Our present analysis reveals the unique protein domain organization of iterative type II PKS and KS domain of marine actinobacteria. The findings of this study would have implications in metabolic pathway reconstruction and design of semi-synthetic genomes to achieve rational design of novel natural products.

  15. Lantibiotics produced by Actinobacteria and their potential applications (a Review).

    PubMed

    Gomes, Karen; Duarte, Rafael Silva; Bastos, Maria do Carmo de Freire

    2016-11-22

    The phylum Actinobacteria, which comprises a great variety of Gram-positive bacteria with a high G+C content in their genomes, is known for its large production of bioactive compounds, including those with antimicrobial activity. Among the antimicrobials, bacteriocins, ribosomally-synthesized peptides, represent an important arsenal of potential new drugs to face the increasing prevalence of resistance to antibiotics among microbial pathogens. The actinobacterial bacteriocins form a heterogeneous group of substances that is difficult to adapt to most proposed classification schemes. However, recent updates have accommodated efficiently the diversity of bacteriocins produced by this phylum. Among the bacteriocins, the lantibiotics represent a source of new antimicrobials to control infections caused mainly by Gram-positive bacteria and with a low propensity for resistance development. Moreover, some of these compounds have additional biological properties, exhibiting activity against viruses and tumor cells, and having also potential to be used in blood pressure or inflammation control and in pain relief. Thus, lantibiotics already described in Actinobacteria exhibit potential practical applications in medical settings, food industry and agriculture, with examples at different stages of pre-clinical and clinical trials.

  16. A novel nucleoid-associated protein specific to the actinobacteria

    PubMed Central

    Swiercz, Julia P.; Nanji, Tamiza; Gloyd, Melanie; Guarné, Alba; Elliot, Marie A.

    2013-01-01

    Effective chromosome organization is central to the functioning of any cell. In bacteria, this organization is achieved through the concerted activity of multiple nucleoid-associated proteins. These proteins are not, however, universally conserved, and different groups of bacteria have distinct subsets that contribute to chromosome architecture. Here, we describe the characterization of a novel actinobacterial-specific protein in Streptomyces coelicolor. We show that sIHF (SCO1480) associates with the nucleoid and makes important contributions to chromosome condensation and chromosome segregation during Streptomyces sporulation. It also affects antibiotic production, suggesting an additional role in gene regulation. In vitro, sIHF binds DNA in a length-dependent but sequence-independent manner, without any obvious structural preferences. It does, however, impact the activity of topoisomerase, significantly altering DNA topology. The sIHF–DNA co-crystal structure reveals sIHF to be composed of two domains: a long N-terminal helix and a C-terminal helix-two turns-helix domain with two separate DNA interaction sites, suggesting a potential role in bridging DNA molecules. PMID:23427309

  17. Microbial community profiling shows dysbiosis in the lesional skin of Vitiligo subjects

    PubMed Central

    Ganju, Parul; Nagpal, Sunil; Mohammed, MH; Nishal Kumar, P; Pandey, Rajesh; Natarajan, Vivek T; Mande, Sharmila S.; Gokhale, Rajesh S.

    2016-01-01

    Healthy human skin harbours a diverse array of microbes that comprise the skin microbiome. Commensal bacteria constitute an important component of resident microbiome and are intricately linked to skin health. Recent studies describe an association between altered skin microbial community and epidemiology of diseases, like psoriasis, atopic dermatitis etc. In this study, we compare the differences in bacterial community of lesional and non-lesional skin of vitiligo subjects. Our study reveals dysbiosis in the diversity of microbial community structure in lesional skin of vitiligo subjects. Although individual specific signature is dominant over the vitiligo-specific microbiota, a clear decrease in taxonomic richness and evenness can be noted in lesional patches. Investigation of community specific correlation networks reveals distinctive pattern of interactions between resident bacterial populations of the two sites (lesional and non-lesional). While Actinobacterial species constitute the central regulatory nodes (w.r.t. degree of interaction) in non-lesional skin, species belonging to Firmicutes dominate on lesional sites. We propose that the changes in taxonomic characteristics of vitiligo lesions, as revealed by our study, could play a crucial role in altering the maintenance and severity of disease. Future studies would elucidate mechanistic relevance of these microbial dynamics that can provide new avenues for therapeutic interventions. PMID:26758568

  18. Delineation of Steroid-Degrading Microorganisms through Comparative Genomic Analysis

    PubMed Central

    Bergstrand, Lee H.; Cardenas, Erick; Holert, Johannes; Van Hamme, Jonathan D.

    2016-01-01

    ABSTRACT Steroids are ubiquitous in natural environments and are a significant growth substrate for microorganisms. Microbial steroid metabolism is also important for some pathogens and for biotechnical applications. This study delineated the distribution of aerobic steroid catabolism pathways among over 8,000 microorganisms whose genomes are available in the NCBI RefSeq database. Combined analysis of bacterial, archaeal, and fungal genomes with both hidden Markov models and reciprocal BLAST identified 265 putative steroid degraders within only Actinobacteria and Proteobacteria, which mainly originated from soil, eukaryotic host, and aquatic environments. These bacteria include members of 17 genera not previously known to contain steroid degraders. A pathway for cholesterol degradation was conserved in many actinobacterial genera, particularly in members of the Corynebacterineae, and a pathway for cholate degradation was conserved in members of the genus Rhodococcus. A pathway for testosterone and, sometimes, cholate degradation had a patchy distribution among Proteobacteria. The steroid degradation genes tended to occur within large gene clusters. Growth experiments confirmed bioinformatic predictions of steroid metabolism capacity in nine bacterial strains. The results indicate there was a single ancestral 9,10-seco-steroid degradation pathway. Gene duplication, likely in a progenitor of Rhodococcus, later gave rise to a cholate degradation pathway. Proteobacteria and additional Actinobacteria subsequently obtained a cholate degradation pathway via horizontal gene transfer, in some cases facilitated by plasmids. Catabolism of steroids appears to be an important component of the ecological niches of broad groups of Actinobacteria and individual species of Proteobacteria. PMID:26956583

  19. Antibacterial and brine shrimp lethality effect of marine actinobacterium Streptomyces sp. CAS72 against human pathogenic bacteria

    PubMed Central

    Sivasankar, Palaniappan; Manivasagan, Panchanathan; Vijayanand, Packiyaraj; Sivakumar, Kannan; Sugesh, Shanmugam; Poongodi, Subramaniam; Maharani, Viswanathan; Vijayalakshmi, Shanmugam; Balasubramanian, Thangavel

    2013-01-01

    Objective To investigate the in vitro antibacterial activity against human pathogenic bacteria and brine shrimp lethality bioassay of the marine actinobacterium. Methods Forty six marine actinobacterial strains were isolated from sediment samples of Uppanar estuary, Cuddalore, India. Preliminary screening was done by cross-streak method and the potential strain was identified by morphological, chemotaxonomical and molecular methods. Fermentation was done and the metabolite was obtained by liquid-liquid extraction using ethyl acetate and purified by silica gel (100-200 mesh) column chromatography. The purified metabolite was tested for antibacterial activity, minimal inhibitory concentration and brine shrimp lethality bioassay. Results Among the forty six strains, CAS72 was found effective against human pathogenic bacteria. The strain CAS72 was identified as Streptomyces sp. The purified metabolite exhibited a significant in vitro antibacterial activity. The MIC value was also determined against human pathogenic bacteria and a strong cytotoxic activity in brine shrimp lethality assay was observed and the LC50 value was 23.5 µg/mL. Conclusions The present investigation reveals that the marine actinobacteria are well obtainable in Uppanar estuary environment and it can provide a definite source for novel bioactive metabolites.

  20. Kocuria arsenatis sp. nov., a novel arsenic-resistant endophytic actinobacterium associated with Prosopis laegivata grown on high arsenic polluted mine tailing in Mexico.

    PubMed

    Román-Ponce, Brenda; Wang, Dan; Vásquez-Murrieta, María Soledad; Chen, Wen Feng; Estrada-de Los Santos, Paulina; Sui, Xin Hua; Wang, En Tao

    2015-12-08

    A Gram positive, aerobic, non-motile, coccoid, arsenic-resistant actinobacterial strain designated as CM1E1T was isolated from the lateral root tissue of Prosopis laegivata grown on a mine tailing in San Luis Potosi, Mexico. Phylogenetic analysis based on 16S rRNA genes revealed that strain CM1E1T was clustered closely with Kocuria species, showing the highest sequence similarity of 98.7 % to Kocuria rhizophila TA68T. The DNA G + C content of strain CM1E1T was 74.5 mol% (Tm). The major fatty acids were anteiso-C15:0, anteiso-C17:0 and iso-C15:0. The peptidoglycan of cell wall contained lysine and alanine. The major respiratory quinones were MK-7 (H2) and MK-8 (H2). On the basis of the phenotypic characterization, phylogenetic relation and chemotaxonomic analyses, strain CM1E1T (=CCBAU 101092T=HAMBI 3625T =LMG 8671T) represents a novel species in genus Kocuria, for which the name Kocuria arsenatis sp. nov is proposed.

  1. Copper removal ability by Streptomyces strains with dissimilar growth patterns and endowed with cupric reductase activity.

    PubMed

    Albarracín, Virginia Helena; Avila, Ana Lucía; Amoroso, María Julia; Abate, Carlos Mauricio

    2008-11-01

    Morphological, physiological and molecular characterization of three copper-resistant actinobacterial strains (AB2A, AB3 and AB5A) isolated from copper-polluted sediments of a drainage channel showed that they belonged to the genus Streptomyces. These characteristics plus their distinctive copper resistance phenotypes revealed considerable divergence among the isolates. Highly dissimilar growth patterns and copper removal efficiency were observed for the selected Streptomyces strains grown on minimal medium (MM) added with 0.5 mM of copper sulfate (MM(Cu)). Strain AB2A showed an early mechanism of copper uptake/retention (80% until day 3), followed by a drastic metal efflux process (days 5-7). In contrast, Streptomyces sp. AB3 and AB5A showed only copper retention phenotypes under the same culture conditions. Particularly, Streptomyces sp. AB5A showed a better efficiency in copper removal (94%), although a longer lag phase was observed for this microorganism grown for 7 days in MM(Cu). Cupric reductase activity was detected in both copper-adapted cells and nonadapted cells of all three strains but this activity was up to 100-fold higher in preadapted cells of Streptomyces sp. AB2A. To our knowledge, this is the first time that cupric reductase activity was demonstrated in Streptomyces strains.

  2. Interaction between workers during a short time window is required for bacterial symbiont transmission in Acromyrmex leaf-cutting ants.

    PubMed

    Marsh, Sarah E; Poulsen, Michael; Pinto-Tomás, Adrián; Currie, Cameron R

    2014-01-01

    Stable associations between partners over time are critical for the evolution of mutualism. Hosts employ a variety of mechanisms to maintain specificity with bacterial associates. Acromyrmex leaf-cutting ants farm a fungal cultivar as their primary nutrient source. These ants also carry a Pseudonocardia Actinobacteria exosymbiont on their bodies that produces antifungal compounds that help inhibit specialized parasites of the ants' fungal garden. Major workers emerge from their pupal cases (eclose) symbiont-free, but exhibit visible Actinobacterial coverage within 14 days post-eclosion. Using subcolony experiments, we investigate exosymbiont transmission within Acromyrmex colonies. We found successful transmission to newly eclosed major workers fostered by major workers with visible Actinobacteria in all cases (100% acquiring, n = 19). In contrast, newly eclosed major workers reared without exosymbiont-carrying major workers did not acquire visible Actinobacteria (0% acquiring, n = 73). We further show that the majority of ants exposed to major workers with exosymbionts within 2 hours of eclosion acquired bacteria (60.7% acquiring, n = 28), while normal acquisition did not occur when exposure occurred later than 2 hours post-eclosion (0% acquiring, n = 18). Our findings show that transmission of exosymbionts to newly eclosed major workers occurs through interactions with exosymbiont-covered workers within a narrow time window after eclosion. This mode of transmission likely helps ensure the defensive function within colonies, as well as specificity and partner fidelity in the ant-bacterium association.

  3. Diversity and bioprospecting of culturable actinomycetes from marine sediment of the Yellow Sea, China.

    PubMed

    Xiong, Zhi-Qiang; Liu, Qiao-Xia; Pan, Zhao-Long; Zhao, Na; Feng, Zhi-Xiang; Wang, Yong

    2015-03-01

    Marine actinomycetes are a potential source of a wide variety of bioactive natural products. In this work, seven pretreatments, three selective isolation media, and five artificial seawater concentrations were used to isolate actinomycetes from the sediments collected from Yellow Sea, China. Statistical analysis showed that only the isolation medium strongly affected the total and bioactive numbers of actinomycete isolates. A total of 613 actinobacterial strains were isolated and screened for antimicrobial activities; 154 isolates showed activity against at least one of nine test drug-resistant microorganisms. Eighty-nine representatives with strong antimicrobial activity were identified phylogenetically based on 16S rRNA gene sequencing, which were assigned to five different actinomycete genera Streptomyces, Kocuria, Saccharomonospora, Micromonospora, and Nocardiopsis. Using PCR-based screening for six biosynthetic genes of secondary metabolites, all 45 isolates with acute activity have at least one biosynthetic gene, 28.8 % of which possess more than three biosynthetic genes. As a case, strain SMA-1 was selected for antimicrobial natural product discovery. Three diketopiperazine dimers including a new compound iso-naseseazine B (1) and two known compounds naseseazine B (2) and aspergilazine A (3) were isolated by bioassay-guided separation. These results suggested that actinomycetes from marine sediments are a potential resource of novel secondary metabolites and drugs.

  4. Exploring the diversity and metabolic potential of actinomycetes from temperate marine sediments from Newfoundland, Canada.

    PubMed

    Duncan, K R; Haltli, B; Gill, K A; Correa, H; Berrué, F; Kerr, R G

    2015-01-01

    Marine sediments from Newfoundland, Canada were explored for biotechnologically promising Actinobacteria using culture-independent and culture-dependent approaches. Culture-independent pyrosequencing analyses uncovered significant actinobacterial diversity (H'-2.45 to 3.76), although the taxonomic diversity of biotechnologically important actinomycetes could not be fully elucidated due to limited sampling depth. Assessment of culturable actinomycete diversity resulted in the isolation of 360 actinomycetes representing 59 operational taxonomic units, the majority of which (94 %) were Streptomyces. The biotechnological potential of actinomycetes from NL sediments was assessed by bioactivity and metabolomics-based screening of 32 representative isolates. Bioactivity was exhibited by 41 % of isolates, while 11 % exhibited unique chemical signatures in metabolomics screening. Chemical analysis of two isolates resulted in the isolation of the cytotoxic metabolite 1-isopentadecanoyl-3β-D-glucopyranosyl-X-glycerol from Actinoalloteichus sp. 2L868 and sungsanpin from Streptomyces sp. 8LB7. These results demonstrate the potential for the discovery of novel bioactive metabolites from actinomycetes isolated from Atlantic Canadian marine sediments.

  5. A Laterally Acquired Galactose Oxidase-Like Gene Is Required for Aerial Development during Osmotic Stress in Streptomyces coelicolor

    PubMed Central

    Liman, Recep; Facey, Paul D.; van Keulen, Geertje; Dyson, Paul J.; Del Sol, Ricardo

    2013-01-01

    Phylogenetic reconstruction revealed that most Actinobacterial orthologs of S. coelicolor SCO2837, encoding a metal-dependent galactose oxidase-like protein, are found within Streptomyces and were probably acquired by horizontal gene transfer from fungi. Disruption of SCO2837 (glxA) caused a conditional bld phenotype that could not be reversed by extracellular complementation. Studies aimed at characterising the regulation of expression of glxA showed that it is not a target for other bld genes. We provide evidence that glxA is required for osmotic adaptation, although independently from the known osmotic stress response element SigB. glxA has been predicted to be part of an operon with the transcription unit comprising the upstream cslA gene and glxA. However, both phenotypic and expression studies indicate that it is also expressed from an independent promoter region internal to cslA. GlxA displays an in situ localisation pattern similar to that one observed for CslA at hyphal tips, but localisation of the former is independent of the latter. The functional role of GlxA in relation to CslA is discussed. PMID:23326581

  6. Properties and Phylogeny of 76 Families of Bacterial and Eukaryotic Organellar Outer Membrane Pore-Forming Proteins

    PubMed Central

    Reddy, Bhaskara L.; Saier, Milton H.

    2016-01-01

    We here report statistical analyses of 76 families of integral outer membrane pore-forming proteins (OMPPs) found in bacteria and eukaryotic organelles. 47 of these families fall into one superfamily (SFI) which segregate into fifteen phylogenetic clusters. Families with members of the same protein size, topology and substrate specificities often cluster together. Virtually all OMPP families include only proteins that form transmembrane pores. Nine such families, all of which cluster together in the SFI phylogenetic tree, contain both α- and β-structures, are multi domain, multi subunit systems, and transport macromolecules. Most other SFI OMPPs transport small molecules. SFII and SFV homologues derive from Actinobacteria while SFIII and SFIV proteins derive from chloroplasts. Three families of actinobacterial OMPPs and two families of eukaryotic OMPPs apparently consist primarily of α-helices (α-TMSs). Of the 71 families of (putative) β-barrel OMPPs, only twenty could not be assigned to a superfamily, and these derived primarily from Actinobacteria (1), chloroplasts (1), spirochaetes (8), and proteobacteria (10). Proteins were identified in which two or three full length OMPPs are fused together. Family characteristic are described and evidence agrees with a previous proposal suggesting that many arose by adjacent β-hairpin structural unit duplications. PMID:27064789

  7. Verrucosispora fiedleri sp. nov., an actinomycete isolated from a fjord sediment which synthesizes proximicins.

    PubMed

    Goodfellow, Michael; Brown, Roselyn; Ahmed, Lina; Pathom-Aree, Wasu; Bull, Alan T; Jones, Amanda L; Stach, James E M; Zucchi, Tiago Domingues; Zhang, Lixin; Wang, Jian

    2013-03-01

    A novel filamentous actinobacterial organism, designated strain MG-37(T), was isolated from a Norwegian fjord sediment and examined using a polyphasic taxonomic approach. The organism was determined to have chemotaxonomic and morphological properties consistent with its classification in the genus Verrucosispora and formed a distinct phyletic line in the Verrucosispora 16S rRNA gene tree. It was most closely related to Verrucosispora maris DSM 45365(T) (99.5 % 16S rRNA gene similarity) and Verrucosispora gifhornensis DSM 44337(T) (99.4 % 16S rRNA gene similarity) but was distinguished from these strains based on low levels of DNA:DNA relatedness (~56 and ~50 %, respectively). It was readily delineated from all of the type strains of Verrucosispora species based on a combination of phenotypic properties. Isolate MG-37(T) (=NCIMB 14794(T) = NRRL-B-24892(T)) should therefore be classified as the type strain of a novel species of Verrucosispora for which the name Verrucosispora fiedleri is proposed.

  8. Phytomonospora cypria sp. nov., isolated from soil.

    PubMed

    Sahin, Nevzat; Veyisoglu, Aysel; Tatar, Demet; Saygin, Hayrettin; Cetin, Demet; Guven, Kiymet; Klenk, Hans-Peter; Goodfellow, Michael

    2015-12-01

    A Gram-stain positive actinobacterial strain, designated KT1403(T), was isolated from a soil sample, collected from Karpaz, Magusa, Northern Cyprus, and characterised using a polyphasic approach. Morphological characteristics and chemotaxonomic data indicated that the strain belongs to the genus Phytomonospora. The cell wall of the novel strain contained meso-diaminopimelic acid and galactose, glucose and mannose as the major sugars in whole cell hydrolysates. The polar lipids in the cell membrane were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, an unidentified aminophospholipid and three unidentified glycolipids. The predominant menaquinones were MK-10(H6) and MK-10(H4). The major fatty acids were found to be iso C15:0 , anteiso C15:0 and anteiso C17:0. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KT1403(T) belongs to the genus Phytomonospora with a sequence similarity of 99.73 % with Phytomonospora endophytica, the type species of the genus. DNA-DNA hybridization further differentiated strain KT1403(T) from its near phylogenetic neighbour, P. endophytica DSM 45386(T) (29.0 ± 2.2 % DNA relatedness). Therefore, it is proposed that strain KT1403(T) represents a novel species of the genus Phytomonospora, for which the name Phytomonospora cypria sp. nov. is proposed. The type strain is KT1403(T) (=KCTC 29479(T) = DSM 46767(T)).

  9. Micromonospora profundi sp. nov., isolated from deep marine sediment.

    PubMed

    Veyisoglu, Aysel; Carro, Lorena; Cetin, Demet; Guven, Kiymet; Spröer, Cathrin; Pötter, Gabriele; Klenk, Hans-Peter; Sahin, Nevzat; Goodfellow, Michael

    2016-11-01

    A novel actinobacterial strain, designated DS3010T, was isolated from a Black Sea marine sediment and characterized using a polyphasic approach. The strain was shown to have chemotaxonomic, morphological and phylogenetic properties consistent with classification as representing a member of the genus Micromonospora. Comparative 16S rRNA gene sequence studies showed that the strain was most closely related to the type strains of Micromonospora saelicesensis (99.5 %), Micromonospora chokoriensis (99.4 %) and Micromonospora violae (99.3 %). Similarly, a corresponding analysis based on partial gyrB gene sequences showed that it formed a distinct phyletic branch in a subclade that included the type strains of Micromonosporazamorensis, 'Micromonospora zeae', 'Micromonospora jinlongensis', M. saelicesensis and Micromonospora lupini. DS3010T was distinguished from its closest phylogenetic neighbours by low levels of DNA-DNA relatedness and by a combination of chemotaxonomic and phenotypic properties. On the basis of these data, it is proposed that the isolate should be assigned to the genus Micromonospora as Micromonospora profundi sp. nov. with isolate DS3010T (=DSM 45981T=KCTC 29243T) as the type strain.

  10. The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon

    PubMed Central

    2011-01-01

    Background The tree of life is usually rooted between archaea and bacteria. We have previously presented three arguments that support placing the root of the tree of life in bacteria. The data have been dismissed because those who support the canonical rooting between the prokaryotic superkingdoms cannot imagine how the vast divide between the prokaryotic superkingdoms could be crossed. Results We review the evidence that archaea are derived, as well as their biggest differences with bacteria. We argue that using novel data the gap between the superkingdoms is not insurmountable. We consider whether archaea are holophyletic or paraphyletic; essential to understanding their origin. Finally, we review several hypotheses on the origins of archaea and, where possible, evaluate each hypothesis using bioinformatics tools. As a result we argue for a firmicute ancestry for archaea over proposals for an actinobacterial ancestry. Conclusion We believe a synthesis of the hypotheses of Lake, Gupta, and Cavalier-Smith is possible where a combination of antibiotic warfare and viral endosymbiosis in the bacilli led to dramatic changes in a bacterium that resulted in the birth of archaea and eukaryotes. Reviewers This article was reviewed by Patrick Forterre, Eugene Koonin, and Gáspár Jékely PMID:21356104

  11. Geodermatophilus saharensis sp. nov., isolated from sand of the Saharan desert in Chad.

    PubMed

    Montero-Calasanz, M C; Göker, M; Pötter, G; Rohde, M; Spröer, C; Schumann, P; Gorbushina, A A; Klenk, H-P

    2013-03-01

    A novel Gram-positive, aerobic, actinobacterial strain, CF5/5, was isolated from soil in the Sahara desert, Chad. It grew best at 20-35 °C and at pH 6.0-8.0 and with 0-4 % (w/v) NaCl, forming black-colored colonies. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the genus Geodermatophilus. The DNA G + C content was 75.9 mol%. The peptidoglycan contained meso-diaminopimelic acid; galactose and xylose were detected as diagnostic sugars. The main phospholipids were diphosphatidylglycerol, phosphatidylcholine, and phosphatidylinositol; MK-9(H(4)) was the dominant menaquinone. The major cellular fatty acids were: iso-C(16:0) and iso-C(15:0). The 16S rRNA gene showed 95.6-98.3 % sequence similarity with the other named members of the genus Geodermatophilus. Based on the polyphasic taxonomy data, the isolate is proposed to represent a novel species, Geodermatophilus saharensis with the type strain CF5/5(T) = DSM 45423 = CCUG 62813 = MTCC 11416.

  12. Carbonate Mineral Formation under the Influence of Limestone-Colonizing Actinobacteria: Morphology and Polymorphism.

    PubMed

    Cao, Chengliang; Jiang, Jihong; Sun, Henry; Huang, Ying; Tao, Faxiang; Lian, Bin

    2016-01-01

    Microorganisms and their biomineralization processes are widespread in almost every environment on earth. In this work, Streptomyces luteogriseus DHS C014, a dominant lithophilous actinobacteria isolated from microbial mats on limestone rocks, was used to investigate its potential biomineralization to allow a better understanding of bacterial contributions to carbonate mineralization in nature. The ammonium carbonate free-drift method was used with mycelium pellets, culture supernatant, and spent culture of the strain. Mineralogical analyses showed that hexagonal prism calcite was only observed in the sub-surfaces of the mycelium pellets, which is a novel morphology mediated by microbes. Hemispheroidal vaterite appeared in the presence of spent culture, mainly because of the effects of soluble microbial products (SMP) during mineralization. When using the culture supernatant, doughnut-like vaterite was favored by actinobacterial mycelia, which has not yet been captured in previous studies. Our analyses suggested that the effects of mycelium pellets as a molecular template almost gained an advantage over SMP both in crystal nucleation and growth, having nothing to do with biological activity. It is thereby convinced that lithophilous actinobacteria, S. luteogriseus DHS C014, owing to its advantageous genetic metabolism and filamentous structure, showed good biomineralization abilities, maybe it would have geoactive potential for biogenic carbonate in local microenvironments.

  13. Ketide Synthase (KS) Domain Prediction and Analysis of Iterative Type II PKS Gene in Marine Sponge-Associated Actinobacteria Producing Biosurfactants and Antimicrobial Agents

    PubMed Central

    Selvin, Joseph; Sathiyanarayanan, Ganesan; Lipton, Anuj N.; Al-Dhabi, Naif Abdullah; Valan Arasu, Mariadhas; Kiran, George S.

    2016-01-01

    The important biological macromolecules, such as lipopeptide and glycolipid biosurfactant producing marine actinobacteria were analyzed and their potential linkage between type II polyketide synthase (PKS) genes was explored. A unique feature of type II PKS genes is their high amino acid (AA) sequence homology and conserved gene organization. These enzymes mediate the biosynthesis of polyketide natural products with enormous structural complexity and chemical nature by combinatorial use of various domains. Therefore, deciphering the order of AA sequence encoded by PKS domains tailored the chemical structure of polyketide analogs still remains a great challenge. The present work deals with an in vitro and in silico analysis of PKS type II genes from five actinobacterial species to correlate KS domain architecture and structural features. Our present analysis reveals the unique protein domain organization of iterative type II PKS and KS domain of marine actinobacteria. The findings of this study would have implications in metabolic pathway reconstruction and design of semi-synthetic genomes to achieve rational design of novel natural products. PMID:26903957

  14. pFiD188, the linear virulence plasmid of Rhodococcus fascians D188.

    PubMed

    Francis, Isolde; De Keyser, Annick; De Backer, Philippe; Simón-Mateo, Carmen; Kalkus, Jutta; Pertry, Ine; Ardiles-Diaz, Wilson; De Rycke, Riet; Vandeputte, Olivier M; El Jaziri, Mondher; Holsters, Marcelle; Vereecke, Danny

    2012-05-01

    Rhodococcus fascians is currently the only phytopathogen of which the virulence genes occur on a linear plasmid. To get insight into the origin of this replicon and into the virulence strategy of this broad-spectrum phytopathogen, the sequence of the linear plasmid of strain D188, pFiD188, was determined. Analysis of the 198,917 bp revealed four syntenic regions with linear plasmids of R. erythropolis, R. jostii, and R. opacus, suggesting a common origin of these replicons. Mutational analysis of pFi_086 and pFi_102, similar to cutinases and type IV peptidases, respectively, showed that conserved region R2 was involved in plasmid dispersal and pointed toward a novel function for actinobacterial cutinases in conjugation. Additionally, pFiD188 had three regions that were unique for R. fascians. Functional analysis of the stk and nrp loci of regions U2 and U3, respectively, indicated that their role in symptom development was limited compared with that of the previously identified fas, att, and hyp virulence loci situated in region U1. Thus, pFiD188 is a typical rhodococcal linear plasmid with a composite structure that encodes core functions involved in plasmid maintenance and accessory functions, some possibly acquired through horizontal gene transfer, implicated in virulence and the interaction with the host.

  15. Characterization of the bacterial community associated with larvae and adults of Anoplophora chinensis collected in Italy by culture and culture-independent methods.

    PubMed

    Rizzi, Aurora; Crotti, Elena; Borruso, Luigimaria; Jucker, Costanza; Lupi, Daniela; Colombo, Mario; Daffonchio, Daniele

    2013-01-01

    The wood-boring beetle Anoplophora chinensis Forster, native to China, has recently spread to North America and Europe causing serious damage to ornamental and forest trees. The gut microbial community associated with these xylophagous beetles is of interest for potential biotechnological applications in lignocellulose degradation and development of pest-control measures. In this study the gut bacterial community of larvae and adults of A. chinensis, collected from different host trees in North Italy, was investigated by both culture and culture-independent methods. Larvae and adults harboured a moderately diverse bacterial community, dominated by Proteobacteria, Actinobacteria, and Firmicutes. The gammaproteobacterial family Enterobacteriaceae (genera Gibbsiella, Enterobacter, Raoultella, and Klebsiella) was the best represented. The abundance of such bacteria in the insect gut is likely due to the various metabolic abilities of Enterobacteriaceae, including fermentation of carbohydrates derived from lignocellulose degradation and contribution to nitrogen intake by nitrogen-fixing activity. In addition, bacteria previously shown to have some lignocellulose-degrading activity were detected at a relatively low level in the gut. These bacteria possibly act synergistically with endogenous and fungal enzymes in lignocellulose breakdown. The detection of actinobacterial symbionts could be explained by a possible role in the detoxification of secondary plant metabolites and/or protection against pathogens.

  16. -Genomic data mining of the marine actinobacteria Streptomyces sp. H-KF8 unveils insights into multi-stress related genes and metabolic pathways involved in antimicrobial synthesis.

    PubMed

    Undabarrena, Agustina; Ugalde, Juan A; Seeger, Michael; Cámara, Beatriz

    2017-01-01

    Streptomyces sp. H-KF8 is an actinobacterial strain isolated from marine sediments of a Chilean Patagonian fjord. Morphological characterization together with antibacterial activity was assessed in various culture media, revealing a carbon-source dependent activity mainly against Gram-positive bacteria (S. aureus and L. monocytogenes). Genome mining of this antibacterial-producing bacterium revealed the presence of 26 biosynthetic gene clusters (BGCs) for secondary metabolites, where among them, 81% have low similarities with known BGCs. In addition, a genomic search in Streptomyces sp. H-KF8 unveiled the presence of a wide variety of genetic determinants related to heavy metal resistance (49 genes), oxidative stress (69 genes) and antibiotic resistance (97 genes). This study revealed that the marine-derived Streptomyces sp. H-KF8 bacterium has the capability to tolerate a diverse set of heavy metals such as copper, cobalt, mercury, chromate and nickel; as well as the highly toxic tellurite, a feature first time described for Streptomyces. In addition, Streptomyces sp. H-KF8 possesses a major resistance towards oxidative stress, in comparison to the soil reference strain Streptomyces violaceoruber A3(2). Moreover, Streptomyces sp. H-KF8 showed resistance to 88% of the antibiotics tested, indicating overall, a strong response to several abiotic stressors. The combination of these biological traits confirms the metabolic versatility of Streptomyces sp. H-KF8, a genetically well-prepared microorganism with the ability to confront the dynamics of the fjord-unique marine environment.

  17. Lantibiotics produced by Actinobacteria and their potential applications (a review).

    PubMed

    Gomes, Karen Machado; Duarte, Rafael Silva; de Freire Bastos, Maria do Carmo

    2017-02-01

    The phylum Actinobacteria, which comprises a great variety of Gram-positive bacteria with a high G+C content in their genomes, is known for its large production of bioactive compounds, including those with antimicrobial activity. Among the antimicrobials, bacteriocins, ribosomally synthesized peptides, represent an important arsenal of potential new drugs to face the increasing prevalence of resistance to antibiotics among microbial pathogens. The actinobacterial bacteriocins form a heterogeneous group of substances that is difficult to adapt to most proposed classification schemes. However, recent updates have accommodated efficiently the diversity of bacteriocins produced by this phylum. Among the bacteriocins, the lantibiotics represent a source of new antimicrobials to control infections caused mainly by Gram-positive bacteria and with a low propensity for resistance development. Moreover, some of these compounds have additional biological properties, exhibiting activity against viruses and tumour cells and having also potential to be used in blood pressure or inflammation control and in pain relief. Thus, lantibiotics already described in Actinobacteria exhibit potential practical applications in medical settings, food industry and agriculture, with examples at different stages of pre-clinical and clinical trials.

  18. Gancidin W, a potential low-toxicity antimalarial agent isolated from an endophytic Streptomyces SUK10

    PubMed Central

    Zin, Noraziah Mohamad; Baba, Mohd Shukri; Zainal-Abidin, Abu Hassan; Latip, Jalifah; Mazlan, Noor Wini; Edrada-Ebel, RuAngelie

    2017-01-01

    Endophytic Streptomyces strains are potential sources for novel bioactive molecules. In this study, the diketopiperazine gancidin W (GW) was isolated from the endophytic actinobacterial genus Streptomyces, SUK10, obtained from the bark of Shorea ovalis tree, and it was tested in vivo against Plasmodium berghei PZZ1/100. GW exhibited an inhibition rate of nearly 80% at 6.25 and 3.125 μg kg−1 body weight on day four using the 4-day suppression test method on male ICR strain mice. Comparing GW at both concentrations with quinine hydrochloride and normal saline as positive and negative controls, respectively, 50% of the mice treated with 3.125 μg kg−1 body weight managed to survive for more than 11 months after infection, which almost reached the life span of normal mice. Biochemical tests of selected enzymes and proteins in blood samples of mice treated with GW were also within normal levels; in addition, no abnormalities or injuries were found on internal vital organs. These findings indicated that this isolated bioactive compound from Streptomyces SUK10 exhibits very low toxicity and is a good candidate for potential use as an antimalarial agent in an animal model. PMID:28223778

  19. Diversity of polyketide synthase genes from bacteria associated with the marine sponge Pseudoceratina clavata: culture-dependent and culture-independent approaches.

    PubMed

    Kim, Tae Kyung; Fuerst, John A

    2006-08-01

    Diverse ketosynthase (KS) genes were retrieved from the microbial community associated with the Great Barrier Reef sponge Pseudoceratina clavata. Bacterial isolation and metagenomic approaches were employed. Phylogenetic analysis of 16S rRNA of culturable sponge-associated bacterial communities comprised eight groups over four phyla. Ten KS domains were amplified from four genera of isolates and phylogenetics demonstrated that these KS domains were located in three clusters (actinobacterial, cyanobacterial and trans-AT type). Metagenomic DNA of the sponge microbial community was extracted to explore community KS genes by two approaches: direct amplification of KS domains and construction of fosmid libraries for KS domain screening. Five KS domains were retrieved from polymerase chain reaction (PCR) amplification using sponge metagenome DNA as template and five fosmid clones containing KS domains found using multiplex PCR screening. Analysis of selected polyketide synthase (PKS) from one fosmid showed that the PKS consists of two modules. Open reading frames located up- and downstream of the PKS displayed similarity with membrane synthesis-related proteins such as cardiolipin synthase. Metagenome approaches did not detect KS domains found in sponge isolates. All KS domains from both metagenome approaches formed a single cluster with KS domains originating from metagenomes derived from other sponge species from other geographical regions.

  20. Carbonate Mineral Formation under the Influence of Limestone-Colonizing Actinobacteria: Morphology and Polymorphism

    PubMed Central

    Cao, Chengliang; Jiang, Jihong; Sun, Henry; Huang, Ying; Tao, Faxiang; Lian, Bin

    2016-01-01

    Microorganisms and their biomineralization processes are widespread in almost every environment on earth. In this work, Streptomyces luteogriseus DHS C014, a dominant lithophilous actinobacteria isolated from microbial mats on limestone rocks, was used to investigate its potential biomineralization to allow a better understanding of bacterial contributions to carbonate mineralization in nature. The ammonium carbonate free-drift method was used with mycelium pellets, culture supernatant, and spent culture of the strain. Mineralogical analyses showed that hexagonal prism calcite was only observed in the sub-surfaces of the mycelium pellets, which is a novel morphology mediated by microbes. Hemispheroidal vaterite appeared in the presence of spent culture, mainly because of the effects of soluble microbial products (SMP) during mineralization. When using the culture supernatant, doughnut-like vaterite was favored by actinobacterial mycelia, which has not yet been captured in previous studies. Our analyses suggested that the effects of mycelium pellets as a molecular template almost gained an advantage over SMP both in crystal nucleation and growth, having nothing to do with biological activity. It is thereby convinced that lithophilous actinobacteria, S. luteogriseus DHS C014, owing to its advantageous genetic metabolism and filamentous structure, showed good biomineralization abilities, maybe it would have geoactive potential for biogenic carbonate in local microenvironments. PMID:27148166

  1. Diversity, ecological distribution and biotechnological potential of Actinobacteria inhabiting seamounts and non-seamounts in the Tyrrhenian Sea.

    PubMed

    Ettoumi, Besma; Chouchane, Habib; Guesmi, Amel; Mahjoubi, Mouna; Brusetti, Lorenzo; Neifar, Mohamed; Borin, Sara; Daffonchio, Daniele; Cherif, Ameur

    2016-01-01

    In the present study, the ecological distribution of marine Actinobacteria isolated from seamount and non-seamount stations in the Tyrrhenian Sea was investigated. A collection of 110 isolates was analyzed by Automated Ribosomal Intergenic Spacer Analysis (ARISA) and 16S rRNA gene sequencing of representatives for each ARISA haplotype (n=49). Phylogenetic analysis of 16S rRNA sequences showed a wide diversity of marine isolates and clustered the strains into 11 different genera, Janibacter, Rhodococcus, Arthrobacter, Kocuria, Dietzia, Curtobacterium, Micrococcus, Citricoccus, Brevibacterium, Brachybacterium and Nocardioides. Interestingly, Janibacter limosus was the most encountered species particularly in seamounts stations, suggesting that it represents an endemic species of this particular ecosystem. The application of BOX-PCR fingerprinting on J. limosus sub-collection (n=22), allowed their separation into seven distinct BOX-genotypes suggesting a high intraspecific microdiversity among the collection. Furthermore, by screening the biotechnological potential of selected actinobacterial strains, J. limosus was shown to exhibit the most important biosurfactant activity. Our overall data indicates that Janibacter is a major and active component of seamounts in the Tyrrhenian Sea adapted to low nutrient ecological niche.

  2. Nocardiopsis sp. SD5: a potent feather degrading rare actinobacterium isolated from feather waste in Tamil Nadu, India.

    PubMed

    Saha, Subhasish; Dhanasekaran, D; Shanmugapriya, S; Latha, S

    2013-07-01

    Feather waste, generated in large quantities as a byproduct of commercial poultry processing, is nearly pure keratin protein, and keratin in its native state is not degradable by common proteolytic enzymes. The aim of the study was to find a potent feather degrading actinobacteria from feather waste soil. Out of 91 actinobacterial isolates recorded from feather waste soil in Tiruchirappalli and Nammakkal District, Tamil Nadu, India, isolate SD5 was selected for characterization because it exhibited significant keratinolytic activity. On the basis of the phenotypic, biochemical characterization and 16S rRNA gene-sequencing studies, the isolate was identified as Nocardiopsis sp. SD5. Protease and keratinase activity of Nocardiopsis sp. SD5 were analyzed. The enzyme was more stable over the neutral pH and the temperature of 40 °C. The optimum temperature and pH for both proteolytic and keratinolytic activity was determined at 50 °C and pH 9, respectively. Enzyme inhibitors, detergents and chelator declined the enzyme activity with increasing concentration. Nondenaturing polyacrylamide gel electrophoresis and zymogram elucidated the presence of 30 and 60 kDa protease enzymes. These findings indicated that thermo alkaliphilic feather degrading strain Nocardiopsis sp. SD5 could be used to control the feather waste pollution and to convert keratin rich feather waste into useful feedstock for poultry industry.

  3. Microbial communities and chemosynthesis in yellowstone lake sublacustrine hydrothermal vent waters.

    PubMed

    Yang, Tingting; Lyons, Shawn; Aguilar, Carmen; Cuhel, Russell; Teske, Andreas

    2011-01-01

    Five sublacustrine thermal spring locations from 1 to 109 m water depth in Yellowstone Lake were surveyed by 16S ribosomal RNA gene sequencing in relation to their chemical composition and dark CO(2) fixation rates. They harbor distinct chemosynthetic bacterial communities, depending on temperature (16-110°C) and electron donor supply (H(2)S <1 to >100 μM; NH(3) <0.5 to >10 μM). Members of the Aquificales, most closely affiliated with the genus Sulfurihydrogenibium, are the most frequently recovered bacterial 16S rRNA gene phylotypes in the hottest samples; the detection of these thermophilic sulfur-oxidizing autotrophs coincided with maximal dark CO(2) fixation rates reaching near 9 μM C h(-1) at temperatures of 50-60°C. Vents at lower temperatures yielded mostly phylotypes related to the mesophilic gammaproteobacterial sulfur oxidizer Thiovirga. In contrast, cool vent water with low chemosynthetic activity yielded predominantly phylotypes related to freshwater Actinobacterial clusters with a cosmopolitan distribution.

  4. Production of α-amylase for the biosynthesis of gold nanoparticles using Streptomyces sp. MBRC-82.

    PubMed

    Manivasagan, Panchanathan; Venkatesan, Jayachandran; Kang, Kyong-Hwa; Sivakumar, Kannan; Park, Sun-Joo; Kim, Se-Kwon

    2015-01-01

    Marine actinobacterial synthesis of gold nanoparticles has good potential to develop simple, cost-effective and eco-friendly methods for production of important biomaterials. In this context, gold nanoparticles have attracted considerable attention in recent years, owing to their various applications. In this paper, we report on the production of α-amylase for the extracellular synthesis of gold nanoparticles using Streptomyces sp. MBRC-82. Medium composition and culture conditions for α-amylase production were statistically optimized. Plackett-Burman design was employed to find out the optimal medium constituents and culture conditions to enhance α-amylase production. Box-Behnken design revealed that three independent variables namely soluble starch (5.8484 g), peptone (3.5191 g), and NaCl (0.3829) significantly influenced α-amylase production. The gold nanoparticles were characterized by ultraviolet-visible (UV-vis) spectrometer, X-ray diffractometer (XRD), Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), energy dispersive X-ray analysis (EDXA), and transmission electron microscopy (TEM). The particles synthesized using the optimized enzyme activity ranged from 20 to 80 nm with an average particle size of 40 nm and therefore can be extended to various medicinal applications.

  5. Pseudonocardia adelaidensis sp. nov., an endophytic actinobacterium isolated from the surface-sterilized stem of a grey box tree (Eucalyptus microcarpa).

    PubMed

    Kaewkla, Onuma; Franco, Christopher M M

    2010-12-01

    An aerobic, actinobacterial strain with rod-shaped spores, EUM 221(T) [corrected], which was isolated from the surface-sterilized stem of a grey box tree (Eucalyptus microcarpa), is described. Phylogenetic evaluation based on 16S rRNA gene sequence similarity showed that this isolate belongs to the family Pseudonocardiaceae, with the closest neighbour being Pseudonocardia zijingensis 6330(T) (98.7 %). The level of 16S rRNA gene sequence similarity between the isolate and species of the genus Pseudonocardia with validly published names ranged from 95 to 98 %. Chemotaxonomic data (meso-diaminopimelic acid; major menaquinone MK-8(H(4)); major fatty acid iso-C(16 : 0)) confirmed the affiliation of strain EUM 221(T) [corrected] to the genus Pseudonocardia. The results of the phylogenetic analysis, including physiological and biochemical studies in combination with DNA-DNA hybridization, allowed the genotypic and phenotypic differentiation of strain EUM 221(T) [corrected] from the closest described species. Therefore, this strain represented a novel species and the name proposed is Pseudonocardia adelaidensis sp. nov. The type strain is EUM 221(T) [corrected] (=DSM 45352(T) =ACM 5286(T)).

  6. Ancient Evolution and Recent Evolution Converge for the Biodegradation of Cyanuric Acid and Related Triazines

    PubMed Central

    Seffernick, Jennifer L.

    2016-01-01

    Cyanuric acid was likely present on prebiotic Earth, may have been a component of early genetic materials, and is synthesized industrially today on a scale of more than one hundred million pounds per year in the United States. In light of this, it is not surprising that some bacteria and fungi have a metabolic pathway that sequentially hydrolyzes cyanuric acid and its metabolites to release the nitrogen atoms as ammonia to support growth. The initial reaction that opens the s-triazine ring is catalyzed by the unusual enzyme cyanuric acid hydrolase. This enzyme is in a rare protein family that consists of only cyanuric acid hydrolase (CAH) and barbiturase, with barbiturase participating in pyrimidine catabolism by some actinobacterial species. The X-ray structures of two cyanuric acid hydrolase proteins show that this family has a unique protein fold. Phylogenetic, bioinformatic, enzymological, and genetic studies are consistent with the idea that CAH has an ancient protein fold that was rare in microbial populations but is currently becoming more widespread in microbial populations in the wake of anthropogenic synthesis of cyanuric acid and other s-triazine compounds that are metabolized via a cyanuric acid intermediate. The need for the removal of cyanuric acid from swimming pools and spas, where it is used as a disinfectant stabilizer, can potentially be met using an enzyme filtration system. A stable thermophilic cyanuric acid hydrolase from Moorella thermoacetica is being tested for this purpose. PMID:26729715

  7. Bacteria abundance and diversity of different life stages of Plutella xylostella (Lepidoptera: Plutellidae), revealed by bacteria culture-dependent and PCR-DGGE methods.

    PubMed

    Lin, Xiao-Li; Pan, Qin-Jian; Tian, Hong-Gang; Douglas, Angela E; Liu, Tong-Xian

    2015-03-01

    Microbial abundance and diversity of different life stages (fourth instar larvae, pupae and adults) of the diamondback moth, Plutella xylostella L., collected from field and reared in laboratory, were investigated using bacteria culture-dependent method and PCR-DGGE analysis based on the sequence of bacteria 16S rRNA V3 region gene. A large quantity of bacteria was found in all life stages of P. xylostella. Field population had higher quantity of bacteria than laboratory population, and larval gut had higher quantity than pupae and adults. Culturable bacteria differed in different life stages of P. xylostella. Twenty-five different bacterial strains were identified in total, among them 20 strains were presented in larval gut, only 8 strains in pupae and 14 strains in adults were detected. Firmicutes bacteria, Bacillus sp., were the most dominant species in every life stage. 15 distinct bands were obtained from DGGE electrophoresis gel. The sequences blasted in GenBank database showed these bacteria belonged to six different genera. Phylogenetic analysis showed the sequences of the bacteria belonged to the Actinobacteri, Proteobacteria and Firmicutes. Serratia sp. in Proteobacteria was the most abundant species in larval gut. In pupae, unculturable bacteria were the most dominant species, and unculturable bacteria and Serratia sp. were the most dominant species in adults. Our study suggested that a combination of molecular and traditional culturing methods can be effectively used to analyze and to determine the diversity of gut microflora. These known bacteria may play important roles in development of P. xylostella.

  8. The Effect of Land Use on Bacterial Communities in Saline-Alkali Soil.

    PubMed

    Peng, Mu; Jia, Hongbai; Wang, Qiuyu

    2017-03-01

    Saline-alkali soil can inhibit the growth of crops as a consequence of cellular damage through oxidation of lipids and proteins and degradation of nucleic acids, ultimately leading to cell death. The bacterial community composition and diversity in saline-alkali soil across different land uses, such as agricultural land, forest land, and grassland, were evaluated using high-throughput sequencing of the bacterial 16S rRNA gene. Significant differences in the soil physicochemical characteristics and bacterial community among different land uses were observed in this study. The soil pH value and electrical conductivity were much higher in grassland soil than in agricultural and forest soils. There were high proportions of Actinobacteria and Proteobacteria (phyla) in agricultural and forest soils, while Actinobacteria, Bacteroidetes, Gemmatimonadetes were more predominant in grassland soil. The relative abundance of dominant taxa exhibited a highly significant correlation with soil pH, water content, EC, and organic matter. The percentage of species that are shared among the different soil samples ranged from 5.3 to 30.5%. The haloalkaliphilic Actinobacterial genus Nitriliruptor was detected in grassland but not in areas with other types of land use. Results of both heatmap and principal component analysis (PCA) indicated that the soil properties and bacterial communities in the areas studied have been greatly influenced by long-term land use by different management.

  9. Micromonospora luteifusca sp. nov. isolated from cultivated Pisum sativum.

    PubMed

    Carro, Lorena; Riesco, Raúl; Spröer, Cathrin; Trujillo, Martha E

    2016-06-01

    Three novel actinobacterial strains, GUI2(T), GUI42 and CR21 isolated from nodular tissues and the rhizosphere of a sweet pea plant collected in Cañizal, Spain were identified according to their 16S rRNA gene sequences as new members of the genus Micromonospora. The closest phylogenetic members were found to be Micromonospora saelicesensis (99.2%) "Micromonospora zeae" (99.1%), "Micromonospora jinlongensis" (99%), Micromonospora lupini (98.9%) and Micromonospora zamorensis (98.8%). To resolve their full taxonomic position, four additional genes (atpD, gyrB, recA, rpoB) were partially sequenced and compared to available Micromonospora type strain sequences. DNA-DNA hybridization, BOX-PCR and ARDRA profiles confirmed that these strains represent a novel genomic species. All strains contained meso-diaminopimelic and hydroxy-diaminopimelic acids in their cell wall. Their fatty acid profiles comprised iso-C15:0, iso-C16:0 and anteiso-C15:0 as major components. The polar lipids diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol were found in the type strain GUI2(T) which also contained MK-10(H4) as the major menaquinone. Physiological and biochemical characteristics also differentiated the new isolates. Based on the integration of the above studies, strains GUI2(T), GUI42 and CR21 represent a novel Micromonospora species and we propose the name Micromonospora luteifusca sp. nov. The type strain is GUI2(T) (=CECT 8846(T); =DSM 100204(T)).

  10. Interaction between Workers during a Short Time Window Is Required for Bacterial Symbiont Transmission in Acromyrmex Leaf-Cutting Ants

    PubMed Central

    Marsh, Sarah E.; Poulsen, Michael; Pinto-Tomás, Adrián; Currie, Cameron R.

    2014-01-01

    Stable associations between partners over time are critical for the evolution of mutualism. Hosts employ a variety of mechanisms to maintain specificity with bacterial associates. Acromyrmex leaf-cutting ants farm a fungal cultivar as their primary nutrient source. These ants also carry a Pseudonocardia Actinobacteria exosymbiont on their bodies that produces antifungal compounds that help inhibit specialized parasites of the ants' fungal garden. Major workers emerge from their pupal cases (eclose) symbiont-free, but exhibit visible Actinobacterial coverage within 14 days post-eclosion. Using subcolony experiments, we investigate exosymbiont transmission within Acromyrmex colonies. We found successful transmission to newly eclosed major workers fostered by major workers with visible Actinobacteria in all cases (100% acquiring, n = 19). In contrast, newly eclosed major workers reared without exosymbiont-carrying major workers did not acquire visible Actinobacteria (0% acquiring, n = 73). We further show that the majority of ants exposed to major workers with exosymbionts within 2 hours of eclosion acquired bacteria (60.7% acquiring, n = 28), while normal acquisition did not occur when exposure occurred later than 2 hours post-eclosion (0% acquiring, n = 18). Our findings show that transmission of exosymbionts to newly eclosed major workers occurs through interactions with exosymbiont-covered workers within a narrow time window after eclosion. This mode of transmission likely helps ensure the defensive function within colonies, as well as specificity and partner fidelity in the ant-bacterium association. PMID:25058579

  11. Characterization of the Bacterial Community Associated with Larvae and Adults of Anoplophora chinensis Collected in Italy by Culture and Culture-Independent Methods

    PubMed Central

    Rizzi, Aurora; Crotti, Elena; Lupi, Daniela; Daffonchio, Daniele

    2013-01-01

    The wood-boring beetle Anoplophora chinensis Forster, native to China, has recently spread to North America and Europe causing serious damage to ornamental and forest trees. The gut microbial community associated with these xylophagous beetles is of interest for potential biotechnological applications in lignocellulose degradation and development of pest-control measures. In this study the gut bacterial community of larvae and adults of A. chinensis, collected from different host trees in North Italy, was investigated by both culture and culture-independent methods. Larvae and adults harboured a moderately diverse bacterial community, dominated by Proteobacteria, Actinobacteria, and Firmicutes. The gammaproteobacterial family Enterobacteriaceae (genera Gibbsiella, Enterobacter, Raoultella, and Klebsiella) was the best represented. The abundance of such bacteria in the insect gut is likely due to the various metabolic abilities of Enterobacteriaceae, including fermentation of carbohydrates derived from lignocellulose degradation and contribution to nitrogen intake by nitrogen-fixing activity. In addition, bacteria previously shown to have some lignocellulose-degrading activity were detected at a relatively low level in the gut. These bacteria possibly act synergistically with endogenous and fungal enzymes in lignocellulose breakdown. The detection of actinobacterial symbionts could be explained by a possible role in the detoxification of secondary plant metabolites and/or protection against pathogens. PMID:24069601

  12. Silencing of cryptic prophages in Corynebacterium glutamicum

    PubMed Central

    Pfeifer, Eugen; Hünnefeld, Max; Popa, Ovidiu; Polen, Tino; Kohlheyer, Dietrich; Baumgart, Meike; Frunzke, Julia

    2016-01-01

    DNA of viral origin represents a ubiquitous element of bacterial genomes. Its integration into host regulatory circuits is a pivotal driver of microbial evolution but requires the stringent regulation of phage gene activity. In this study, we describe the nucleoid-associated protein CgpS, which represents an essential protein functioning as a xenogeneic silencer in the Gram-positive Corynebacterium glutamicum. CgpS is encoded by the cryptic prophage CGP3 of the C. glutamicum strain ATCC 13032 and was first identified by DNA affinity chromatography using an early phage promoter of CGP3. Genome-wide profiling of CgpS binding using chromatin affinity purification and sequencing (ChAP-Seq) revealed its association with AT-rich DNA elements, including the entire CGP3 prophage region (187 kbp), as well as several other elements acquired by horizontal gene transfer. Countersilencing of CgpS resulted in a significantly increased induction frequency of the CGP3 prophage. In contrast, a strain lacking the CGP3 prophage was not affected and displayed stable growth. In a bioinformatics approach, cgpS orthologs were identified primarily in actinobacterial genomes as well as several phage and prophage genomes. Sequence analysis of 618 orthologous proteins revealed a strong conservation of the secondary structure, supporting an ancient function of these xenogeneic silencers in phage-host interaction. PMID:27492287

  13. Pupylated proteins in Corynebacterium glutamicum revealed by MudPIT analysis.

    PubMed

    Küberl, Andreas; Fränzel, Benjamin; Eggeling, Lothar; Polen, Tino; Wolters, Dirk Andreas; Bott, Michael

    2014-06-01

    In a manner similar to ubiquitin, the prokaryotic ubiquitin-like protein (Pup) has been shown to target proteins for degradation via the proteasome in mycobacteria. However, not all actinobacteria possessing the Pup protein also contain a proteasome. In this study, we set out to study pupylation in the proteasome-lacking non-pathogenic model organism Corynebacterium glutamicum. A defined pup deletion mutant of C. glutamicum ATCC 13032 grew aerobically as the parent strain in standard glucose minimal medium, indicating that pupylation is dispensable under these conditions. After expression of a Pup derivative carrying an aminoterminal polyhistidine tag in the Δpup mutant and Ni(2+)-chelate affinity chromatography, pupylated proteins were isolated. Multidimensional protein identification technology (MudPIT) and MALDI-TOF-MS/MS of the elution fraction unraveled 55 proteins being pupylated in C. glutamicum and 66 pupylation sites. Similar to mycobacteria, the majority of pupylated proteins are involved in metabolism or translation. Our results define the first pupylome of an actinobacterial species lacking a proteasome, confirming that other fates besides proteasomal degradation are possible for pupylated proteins.

  14. Silencing of cryptic prophages in Corynebacterium glutamicum.

    PubMed

    Pfeifer, Eugen; Hünnefeld, Max; Popa, Ovidiu; Polen, Tino; Kohlheyer, Dietrich; Baumgart, Meike; Frunzke, Julia

    2016-12-01

    DNA of viral origin represents a ubiquitous element of bacterial genomes. Its integration into host regulatory circuits is a pivotal driver of microbial evolution but requires the stringent regulation of phage gene activity. In this study, we describe the nucleoid-associated protein CgpS, which represents an essential protein functioning as a xenogeneic silencer in the Gram-positive Corynebacterium glutamicum CgpS is encoded by the cryptic prophage CGP3 of the C. glutamicum strain ATCC 13032 and was first identified by DNA affinity chromatography using an early phage promoter of CGP3. Genome-wide profiling of CgpS binding using chromatin affinity purification and sequencing (ChAP-Seq) revealed its association with AT-rich DNA elements, including the entire CGP3 prophage region (187 kbp), as well as several other elements acquired by horizontal gene transfer. Countersilencing of CgpS resulted in a significantly increased induction frequency of the CGP3 prophage. In contrast, a strain lacking the CGP3 prophage was not affected and displayed stable growth. In a bioinformatics approach, cgpS orthologs were identified primarily in actinobacterial genomes as well as several phage and prophage genomes. Sequence analysis of 618 orthologous proteins revealed a strong conservation of the secondary structure, supporting an ancient function of these xenogeneic silencers in phage-host interaction.

  15. Bifidobacterium lemurum sp. nov., from faeces of the ring-tailed lemur (Lemur catta).

    PubMed

    Modesto, Monica; Michelini, Samanta; Stefanini, Ilaria; Sandri, Camillo; Spiezio, Caterina; Pisi, Annamaria; Filippini, Gianfranco; Biavati, Bruno; Mattarelli, Paola

    2015-06-01

    Four Gram-positive-staining, microaerophilic, non-spore-forming, fructose-6-phosphate phosphoketolase-positive bacterial strains were isolated from a faecal sample of a 5-year-old ring-tailed lemur (Lemur catta). The strains showed a peculiar morphology, resembling a small coiled snake, a ring shape, or forming a little 'Y' shape. The isolated strains appeared identical, and LMC 13T was chosen as a representative strain and characterized further. Strain LMC 13T showed an A3β peptidoglycan type, similar to that found in Bifidobacterium longum. The DNA base composition was 57.2 mol% G+C. Almost-complete 16S rRNA, hsp60, rpoB, dnaJ, dnaG, purF, clpC and rpoC gene sequences were obtained, and phylogenetic relationships were determined. Comparative analysis of 16S rRNA gene sequences showed that strain LMC 13T showed the highest similarity to B. longum subsp. suis ATCC 27533T (96.65 %) and Bifidobacterium saguini DSM 23967T (96.64 %). Strain LMC 13T was located in an actinobacterial cluster and was more closely related to the genus Bifidobacteriumthan to other genera in the Bifidobacteriaceae. On the basis of these results, strain LMC 13T represents a novel species within the genus Bifidobacterium, for which the name Bifidobacterium lemurum sp. nov. is proposed; the type strain is LMC 13T ( = DSM 28807T = JCM 30168T).

  16. Protease Inhibitors from Marine Actinobacteria as a Potential Source for Antimalarial Compound

    PubMed Central

    Karthik, L.; Kumar, Gaurav; Keswani, Tarun; Bhattacharyya, Arindam; Chandar, S. Sarath; Bhaskara Rao, K. V.

    2014-01-01

    The study was planned to screen the marine actinobacterial extract for the protease inhibitor activity and its anti- Pf activity under in vitro and in vivo conditions. Out of 100 isolates, only 3 isolates exhibited moderate to high protease inhibitor activities on trypsin, chymotrypsin and proteinase K. Based on protease inhibitor activity 3 isolates were chosen for further studies. The potential isolate was characterized by polyphasic approach and identified as Streptomyces sp LK3 (JF710608). The lead compound was identified as peptide from Streptomyces sp LK3. The double-reciprocal plot displayed inhibition mode is non-competitive and it confirms the irreversible nature of protease inhibitor. The peptide from Streptomyces sp LK3 extract showed significant anti plasmodial activity (IC50: 25.78 µg/ml). In in vivo model, the highest level of parasitemia suppression (≈45%) was observed in 600 mg/kg of the peptide. These analyses revealed no significant changes were observed in the spleen and liver tissue during 8 dpi. The results confirmed up-regulation of TGF-β and down regulation of TNF-α in tissue and serum level in PbA infected peptide treated mice compared to PbA infection. The results obtained infer that the peptide possesses anti- Pf activity activity. It suggests that the extracts have novel metabolites and could be considered as a potential source for drug development. PMID:24618707

  17. Intracellular Accumulation of Glycine in Polyphosphate-Accumulating Organisms in Activated Sludge, a Novel Storage Mechanism under Dynamic Anaerobic-Aerobic Conditions

    PubMed Central

    Nguyen, Hien Thi Thu; Kristiansen, Rikke; Vestergaard, Mette; Wimmer, Reinhard

    2015-01-01

    Dynamic anaerobic-aerobic feast-famine conditions are applied to wastewater treatment plants to select polyphosphate-accumulating organisms to carry out enhanced biological phosphorus removal. Acetate is a well-known substrate to stimulate this process, and here we show that different amino acids also are suitable substrates, with glycine as the most promising. 13C-labeled glycine and nuclear magnetic resonance (NMR) were applied to investigate uptake and potential storage products when activated sludge was fed with glycine under anaerobic conditions. Glycine was consumed by the biomass, and the majority was stored intracellularly as free glycine and fermentation products. Subsequently, in the aerobic phase without addition of external substrate, the stored glycine was consumed. The uptake of glycine and oxidation of intracellular metabolites took place along with a release and uptake of orthophosphate, respectively. Fluorescence in situ hybridization combined with microautoradiography using 3H-labeled glycine revealed uncultured actinobacterial Tetrasphaera as a dominant glycine consumer. Experiments with Tetrasphaera elongata as representative of uncultured Tetrasphaera showed that under anaerobic conditions it was able to take up labeled glycine and accumulate this and other labeled metabolites to an intracellular concentration of approximately 4 mM. All components were consumed under subsequent aerobic conditions. Intracellular accumulation of amino acids seems to be a novel storage strategy for polyphosphate-accumulating bacteria under dynamic anaerobic-aerobic feast-famine conditions. PMID:25956769

  18. Genomics of Aerobic Cellulose Utilization Systems in Actinobacteria

    PubMed Central

    Anderson, Iain; Abt, Birte; Lykidis, Athanasios; Klenk, Hans-Peter; Kyrpides, Nikos; Ivanova, Natalia

    2012-01-01

    Cellulose degrading enzymes have important functions in the biotechnology industry, including the production of biofuels from lignocellulosic biomass. Anaerobes including Clostridium species organize cellulases and other glycosyl hydrolases into large complexes known as cellulosomes. In contrast, aerobic actinobacteria utilize systems comprised of independently acting enzymes, often with carbohydrate binding domains. Numerous actinobacterial genomes have become available through the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. We identified putative cellulose-degrading enzymes belonging to families GH5, GH6, GH8, GH9, GH12, GH48, and GH51 in the genomes of eleven members of the actinobacteria. The eleven organisms were tested in several assays for cellulose degradation, and eight of the organisms showed evidence of cellulase activity. The three with the highest cellulase activity were Actinosynnema mirum, Cellulomonas flavigena, and Xylanimonas cellulosilytica. Cellobiose is known to induce cellulolytic enzymes in the model organism Thermobifida fusca, but only Nocardiopsis dassonvillei showed higher cellulolytic activity in the presence of cellobiose. In T. fusca, cellulases and a putative cellobiose ABC transporter are regulated by the transcriptional regulator CelR. Nine organisms appear to use the CelR site or a closely related binding site to regulate an ABC transporter. In some, CelR also regulates cellulases, while cellulases are controlled by different regulatory sites in three organisms. Mining of genome data for cellulose degradative enzymes followed by experimental verification successfully identified several actinobacteria species which were not previously known to degrade cellulose as cellulolytic organisms. PMID:22723998

  19. Influence of transition metals on Streptomyces coelicolor and S. sioyaensis and generation of chromate-reducing mutants.

    PubMed

    Gren, Tetiana; Ostash, Bohdan; Hrubskyy, Yaroslav; Tistechok, Stepan; Fedorenko, Victor

    2014-03-01

    Bacteria-assisted bioremediation is widely recognized as a low-cost method to minimize the consequences of soil pollution with toxic metals originating from industrial sites. Strains used in bioremediation have to deal with high metal load via biosorption, reduction, bioprecipitation, metal sequestration, and/or chelation. Actinobacteria, and streptomycetes in particular, are considered a perspective group for bioremediation as natural soil inhabitants with extensive secondary metabolism. Nevertheless, there is no reference information on survival of the model streptomycetes in the presence of the most abundant metal pollutants. Also, there are no reports describing the selection approaches towards improvement of bioremediation properties. In this work, the resistance of Streptomyces coelicolor M145 and Streptomyces sioyaensis Lv81 to certain transition metals and their growth under different pH values are described for the first time. Spontaneous chromate-resistant S. sioyaensis Lv81-138 strain was selected in the course of this work. Strain Lv81-138 is the most efficient actinobacterial Cr(VI) reducer reported so far, capable of converting 12 mmol/L of Cr(VI) into Cr(III) in a medium supplemented with 50 mmol/L K2CrO4.

  20. The genetic basis for the biosynthesis of the pharmaceutically important class of epoxyketone proteasome inhibitors

    PubMed Central

    Schorn, Michelle; Zettler, Judith; Noel, Joseph P.; Dorrestein, Pieter C.; Moore, Bradley S.; Kaysser, Leonard

    2013-01-01

    The epoxyketone proteasome inhibitors are an established class of therapeutic agents for the treatment of cancer. Their unique α′,β′-epoxyketone pharmacophore allows binding to the catalytic β-subunits of the proteasome with extraordinary specificity. Here we report the characterization of the first gene clusters for the biosynthesis of natural peptidyl-epoxyketones. The clusters for epoxomicin, the lead compound for the anti-cancer drug Kyprolis™, and for eponemycin were identified in the actinobacterial producer strains ATCC 53904 and Streptomyces hygroscopicus ATCC 53709, respectively, using a modified protocol for Ion Torrent PGM genome sequencing. Both gene clusters code for a hybrid non-ribosomal peptide synthetase/polyketide synthase multifunctional enzyme complex and homologous redox enzymes. Epoxomicin and eponemycin were heterologously produced in Streptomyces albus J1046 via whole pathway expression. Moreover, we employed mass spectral molecular networking for a new comparative metabolomics approach in a heterologous system and discovered a number of putative epoxyketone derivatives. With this study we have definitively linked epoxyketone proteasome inhibitors and their biosynthesis genes for the first time in any organism, which will now allow for their detailed biochemical investigation. PMID:24168704

  1. Aalenian foraminiferal fauna and microfacies analyses of the Tethys Ocean Basin from the Transdanubian Range (Hungary)

    NASA Astrophysics Data System (ADS)

    Zsiborás, Gábor; Görög, Ágnes

    2016-04-01

    The early Middle Jurassic foraminiferal fauna of the Tethys Ocean Basin is hardly known. It is especially true for the Aalenian from when only Monaco et al. (1994) published some forms from Valdorbia Section, Central Italy and Wernli (1988) from Domuz Dag, Turkey. Thus the aim of our study was to give a detailed systematic description of the foraminiferal fauna and microfacies analyses of Nagy-Pisznice Section of Lábatlan and T?zköves Gorge of Bakonycsernye from the Transdanubian Range. According to several studies of Géczy} and others, the ammonite fauna indicate all Aalenian (Opalinum, Murchisonae, Concavum) biozones in both successions. 6 samples from T?zköves Gorge, 13 samples from Nagy-Pisznice were collected. Both sequences are about 3 metres thick Ammonitico Rosso type reddish grey limestone with flaser beds and nodules (Tölgyhát Limestone Formation). For the microfacies studies thin sections were made. The dominant microfacies is bioclastic wackestone predominated {Bositra} shells. To extract the microfossils, each sample was dissolved in glacial acetic acid. The microfauna consist of foraminifers, calcispheres, juvenile ammonites, ostracods, radiolarians, microgastropods and fragments of echinoderms. Throughout the Nagy-Pisznice succession, the composition of the foraminiferal fauna is relatively uniform and moderately divers. Most specimens belong to Suborder Lagenina with 60-80{%} abundance. The Suborder Spirillinina are also frequent with 20-35{%} abundance. Agglutinants are subordinated and Suborder Miliolina is absent. The most abundant genus is {Lenticulina}, its amount is more than 50{%} in some samples. {Astacolus}, {Marginulina}, {Dentalina}, {Nodosaria}, {Paralingulina} and Epistominidae are also frequent. {Eoguttulina} and {Paalzowella} are scarce. Spirillinids are represented by {Spirillina}, {Turrispirillina}, and {Coronipora} genera. The taxonomic composition of the foraminiferal fauna of T?zköves Gorge is similar to the aforesaid

  2. Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation

    PubMed Central

    2011-01-01

    Background Freshwater harbors approximately 12,000 fish species accounting for 43% of the diversity of all modern fish. A single ancestral lineage evolved into about two-thirds of this enormous biodiversity (≈ 7900 spp.) and is currently distributed throughout the world's continents except Antarctica. Despite such remarkable species diversity and ubiquity, the evolutionary history of this major freshwater fish clade, Otophysi, remains largely unexplored. To gain insight into the history of otophysan diversification, we constructed a timetree based on whole mitogenome sequences across 110 species representing 55 of the 64 families. Results Partitioned maximum likelihood analysis based on unambiguously aligned sequences (9923 bp) confidently recovered the monophyly of Otophysi and the two constituent subgroups (Cypriniformes and Characiphysi). The latter clade comprised three orders (Gymnotiformes, Characiformes, Siluriformes), and Gymnotiformes was sister to the latter two groups. One of the two suborders in Characiformes (Characoidei) was more closely related to Siluriformes than to its own suborder (Citharinoidei), rendering the characiforms paraphyletic. Although this novel relationship did not receive strong statistical support, it was supported by analyzing independent nuclear markers. A relaxed molecular clock Bayesian analysis of the divergence times and reconstruction of ancestral habitats on the timetree suggest a Pangaean origin and Mesozoic radiation of otophysans. Conclusions The present timetree demonstrates that survival of the ancestral lineages through the two consecutive mass extinctions on Pangaea, and subsequent radiations during the Jurassic through early Cretaceous shaped the modern familial diversity of otophysans. This evolutionary scenario is consistent with recent arguments based on biogeographic inferences and molecular divergence time estimates. No fossil otophysan, however, has been recorded before the Albian, the early Cretaceous 100

  3. Benthic foraminiferal biostratigraphy of the Aalenian-Bajocian (Middle Jurassic) boundary in the Barranco de Agua Larga section (Betic Cordillera, southern Spain)

    NASA Astrophysics Data System (ADS)

    Silva, Sílvia; Canales, María Luisa; Sandoval, José; Henriques, Maria Helena

    2016-04-01

    This work describes the benthic foraminiferal assemblages recorded across the Aalenian - Bajocian boundary in the Barranco de Agua Larga section (Betic Cordillera, SE of Spain), where the ammonite record has enabled the recognition of the Gigantea Subzone in the Bradfordensis Zone (Middle Aalenian), the Concavum and Limitatum subzones in the Concavum Zone (Upper Aalenian) and the Discites Zone (Lower Bajocian). This reference section is characterized by an alternation of limestones and marly limestones corresponding to distal marine environmental conditions, where a total of 17 samples have been collected. They have provided abundant and diverse foraminiferal assemblages, constituted by well-preserved specimens displaying close similarities to those already described for the Jurassic carbonate platforms of the Boreal Realm. From the study of the samples, a total of 3139 specimens have been obtained, corresponding to 5 suborders, 11 families, 25 genus and 80 species. The representatives of the Suborder Lagenina are the most abundant, Vaginulinidae is the most abundant family and Lenticulina is the most abundant genus. From a specific level, the most abundant species are Thurammina jurensis (Franke), Lenticulina muensteri (Roemer) and Prodentalina pseudocommunis (Franke). The occurrence of Astacolus dorbignyi (Roemer) in the Gigantea Subzone has enabled the recognition of the Astacolus dorbignyi Zone. The first occurrence of Lenticulina quenstedti (Gümbel) in the Concavum Subzone has allowed the recognition of the Lenticulina quenstedti Zone. In Barranco de Agua Larga section this species co-occur with Ramulina spandeli Paalzow, the index fossil used in the establishment of the Ramulina spandeli Zone. This zone was defined in the lower part of the Discites Zone in the Murtinheira section (the Bajocian GSSP) and related to distal platform conditions. In the Iberian Basin the Ramulina spandeli Zone was recognized in the Hontoria del Pinar section, but not in the

  4. Lactation in whales and dolphins: evidence of divergence between baleen- and toothed-species.

    PubMed

    Oftedal, O T

    1997-07-01

    Although it has been more than one hundred years since the first publication on the milks of whales and dolphins (Order Cetacea), information on lactation in these species is scattered and fragmentary. Yet the immense size of some cetaceans, and the recent evidence that another group of marine mammals, the true seals, have remarkable rates of secretion of milk fat and energy, make this group of great comparative interest. In this paper information on lactation patterns, milk composition and lactation performance is reviewed. Two very different patterns are evident. Many of the baleen whales (Suborder Mysticeti) have relatively brief lactations (5-7 months) during which they fast or eat relatively little. At mid-lactation they produce milks relatively low in water (40-53%), high in fat (30-50%), and moderately high in protein (9-15%) and ash (1.2-2.1%). From mammary gland weights and postnatal growth rates, it is predicted that their energy outputs in milk are exceptional, reaching on the order of 4000 MJ/ d in the blue whale. This is possible because pregnant females migrate to feeding grounds where they can ingest and deposit great amounts of energy, building up blubber stores prior to parturition. On the other hand, the toothed whales and dolphins (Suborder Odontoceti) have much more extensive lactations typically lasting 1-3 years, during which the mothers feed. At mid-lactation their milks appear to be higher in water (60-77%) and lower in fat (10-30%) and ash (0.6-1.1%), with similar levels of protein (8-11%). At least some odontocetes resemble primates in terms of low predicted rates of energy output and a long period of dependency of the young. However, these hypotheses are based on small numbers of samples for a relatively small number of species. Much of the available data on milk composition is of rather poor quality; for example, it is not possible to determine if milk composition changes over the course of lactation among odontocetes. Additional

  5. Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) using a multigene approach; the effect of data partitioning on resolving phylogenies in a Bayesian framework.

    PubMed

    Strugnell, Jan; Norman, Mark; Jackson, Jennifer; Drummond, Alexei J; Cooper, Alan

    2005-11-01

    rates of evolution than the Octopodiformes. The following taxonomic conclusions are drawn from our analyses: (1) the order Octopoda and suborders Cirrata, Incirrata, and Oegopsida are monophyletic groups; (2) the family Spirulidae (Ram's horn squids) are the sister taxon to the family Sepiidae (cuttlefishes); (3) the family Octopodidae, as currently defined, is paraphyletic; (4) the superfamily Argonautoidea are basal within the suborder Incirrata; and (5) the benthic octopus genera Benthoctopus and Enteroctopus are sister taxa.

  6. Interordinal mammalian relationships: evidence for paenungulate monophyly is provided by complete mitochondrial 12S rRNA sequences.

    PubMed

    Lavergne, A; Douzery, E; Stichler, T; Catzeflis, F M; Springer, M S

    1996-10-01

    The complete mitochondrial 12S rRNA sequences of 5 placental mammals belonging to the 3 orders Sirenia, Proboscidea, and Hyracoidea are reported together with phylogenetic analyses (distance and parsimony) of a total of 51 mammalian orthologues. This 12S rRNA database now includes the 2 extant proboscideans (the African and Asiatic elephants Loxodonta africana and Elephas maximus), 2 of the 3 extant sirenian genera (the sea cow Dugong dugon and the West Indian manatee Trichechus manatus), and 2 of the 3 extant hyracoid genera (the rock and tree hyraxes Procavia capensis and Dendrohyrax dorsalis). The monophyly of the 3 orders Sirenia, Proboscidea, and Hyracoidea is supported by all kinds of analysis. There are 23 and 3 diagnostic subsitutions shared by the 2 proboscideans and the 2 hyracoids, respectively, but none by the 2 sirenians. The 2 proboscideans exhibit the fastest rates of 12S rRNA evolution among the 11 placental orders studied. Based on various taxonomic sampling methods among eutherian orders and marsupial outgroups, the most strongly supported clade in our comparisons clusters together the 3 orders Sirenia, Proboscidea, and Hyracoidea in the superorder Paenungulata. Within paenungulates, the grouping of sirenians and proboscideans within the mirorder Tethytheria is observed. This branching pattern is supported by all analyses by high bootstrap percentages (BPs) and decay indices. When only one species is selected per order or suborder, the taxonomic sampling leads to a relative variation in bootstrap support of 53% for Tethytheria (BPs ranging from 44 to 93%) and 7% for Paernungulata (92-99%). When each order or suborder is represented by two species, this relative variation decreased to 10% for Tethytheria (78-87%) and 3% for Paenungulata (96-99%). Two nearly exclusive synapomorphies for paenungulates are identified in the form of one transitional compensatory change, but none were detected for tethytherians. Such a robust and reliable resolution of

  7. Evolutionary origins of ultrasonic hearing and laryngeal echolocation in bats inferred from morphological analyses of the inner ear

    PubMed Central

    2013-01-01

    Introduction Many mammals have evolved highly adapted hearing associated with ecological specialisation. Of these, bats possess the widest frequency range of vocalisations and associated hearing sensitivities, with frequencies of above 200 kHz in some lineages that use laryngeal echolocation. High frequency hearing in bats appears to have evolved via structural modifications of the inner ear, however, studying these minute features presents considerable challenges and hitherto few such attempts have been made. To understand these adaptations more fully, as well as gain insights into the evolutionary origins of ultrasonic hearing and echolocation in bats, we undertook micro-computed tomography (μCT) scans of the cochleae of representative bat species from 16 families, encompassing their broad range of ecological diversity. To characterise cochlear gross morphology, we measured the relative basilar membrane length and number of turns, and compared these values between echolocating and non-echolocating bats, as well as other mammals. Results We found that hearing and echolocation call frequencies in bats correlated with both measures of cochlear morphology. In particular, relative basilar membrane length was typically longer in echolocating species, and also correlated positively with the number of cochlear turns. Ancestral reconstructions of these parameters suggested that the common ancestor of all extant bats was probably capable of ultrasonic hearing; however, we also found evidence of a significant decrease in the rate of morphological evolution of the basilar membrane in multiple ancestral branches within the Yangochiroptera suborder. Within the echolocating Yinpterochiroptera, there was some evidence of an increase in the rate of basilar membrane evolution in some tips of the tree, possibly associated with reported shifts in call frequency associated with recent speciation events. Conclusions The two main groups of echolocating bat were found to display

  8. COI-based DNA barcoding of some species of Pentatomidae from North India (Hemiptera: Heteroptera).

    PubMed

    Kaur, Harbhajan; Sharma, Kanu

    2016-05-14

    The family Pentatomidae is one of the largest families of the sub-order Heteroptera, comprising 4722 species belonging to 896 genera. In the present paper, we analysed a partial ∼600 bp COI sequence of 14 species of family Pentatomidae, collected from northern part of India. For seven species viz., Tolumnia antennata Distant, 1902, Cahara jugatoria (Lethierry, 1891), Bagrada hilaris (Burmeister, 1835), Plautia viridicollis (Westwood, 1837), Priassus exemptus (Walker, 1868), Dalpada neoclavata (Rider, 1998) and Dalpada affinis (Dallas, 1851), this is the first ever molecular study which has generated distinct barcodes for each. The COI sequences of these seven species have been added to the existing database at GenBank NCBI which can be used for their identification. The database analysis shows mean K2P divergence of 2.5% at intraspecific level, 11.9% at interspecific level and 16.37% at intergeneric level, thereby indicating a hierarchical increase in K2P mean divergence across different taxonomic levels.

  9. Modulation of thermal noise and spectral sensitivity in Lake Baikal cottoid fish rhodopsins

    NASA Astrophysics Data System (ADS)

    Luk, Hoi Ling; Bhattacharyya, Nihar; Montisci, Fabio; Morrow, James M.; Melaccio, Federico; Wada, Akimori; Sheves, Mudi; Fanelli, Francesca; Chang, Belinda S. W.; Olivucci, Massimo

    2016-12-01

    Lake Baikal is the deepest and one of the most ancient lakes in the world. Its unique ecology has resulted in the colonization of a diversity of depth habitats by a unique fauna that includes a group of teleost fish of the sub-order Cottoidei. This relatively recent radiation of cottoid fishes shows a gradual blue-shift in the wavelength of the absorption maximum of their visual pigments with increasing habitat depth. Here we combine homology modeling and quantum chemical calculations with experimental in vitro measurements of rhodopsins to investigate dim-light adaptation. The calculations, which were able to reproduce the trend of observed absorption maxima in both A1 and A2 rhodopsins, reveal a Barlow-type relationship between the absorption maxima and the thermal isomerization rate suggesting a link between the observed blue-shift and a thermal noise decrease. A Nakanishi point-charge analysis of the electrostatic effects of non-conserved and conserved amino acid residues surrounding the rhodopsin chromophore identified both close and distant sites affecting simultaneously spectral tuning and visual sensitivity. We propose that natural variation at these sites modulate both the thermal noise and spectral shifting in Baikal cottoid visual pigments resulting in adaptations that enable vision in deep water light environments.

  10. Harvestman (Opiliones) fauna associated with Maine lowbush blueberry fields in the major production areas of Washington and Hancock counties.

    PubMed

    Drummond, F A; Collins, J A; Choate, B; Woodman, D; Jennings, D T; Forsythe, H Y; Cokendolpher, J C

    2010-10-01

    Over a period of 19 yr, the harvestman (Opiliones) community associated with the lowbush blueberry agro-ecosystem in Maine was studied. Eight species representing five genera, four subfamilies, and two families of harvestmen belonging to the suborder Eupnoi were collected. The harvestman community was dominated by two introduced, synanthropic species: Phalangium opilio in all but 1 yr (that year dominated by Rilaena triangularis). Rilaena was recorded for the first time from eastern North America. Relative abundance of harvestman adults increases throughout the season and the temporal pattern of trap capture does not refute speculated life cycles of the harvestmen being univoltine with overwintering eggs. Some blueberry management practices were found to affect trap capture. We did find that on average (with opposite results 1 yr) trap captures are greater in pruned fields than in fruit-bearing fields. Organic fields were found to have higher relative abundance of harvestmen than conventionally managed fields. Conventionally managed fields with reduced-risk insecticides showed no difference in harvestmen relative abundance compared with those conventionally managed fields using the older more persistent organophosphate insecticides. Insecticide trials with common insecticides used in blueberry insect pest management showed that the organophosphate insecticide, phosmet, and the pyrethroid insecticide, esfenvalerate, were detrimental to P. opilio adults when exposed to leaf residues, whereas the reduced-risk insecticide, spinosad, showed no negative effects compared with nonsprayed foliage.

  11. Molecular data do not provide unambiguous support for the monophyly of flatfishes (Pleuronectiformes): a reply to Betancur-R and Ortí.

    PubMed

    Campbell, Matthew A; Chen, Wei-Jen; López, J Andrés

    2014-06-01

    Betancur-R and Ortí (2014) offer a criticism of our recent examination of the monophyly of extant flatfishes (Pleuronectiformes; Campbell et al., 2013). We welcome this opportunity to examine and respond to the main issues presented in Betancur-R and Ortí (2014). Briefly, this debate centers on the question of whether or not analyses of the available evidence support a stable and confident conclusion regarding a sister group relationship between the two recognized pleuronectiform suborders: Psettodoidei (four species) and Pleuronectoidei (>700 species). In Campbell et al. (2013), we reported results based on sequences from six nuclear genes compatible with monophyly of Pleuronectoidei but not with that of Pleuronectiformes. In our analyses, the most closely related percomorph family to the Pleuronectoidei was resolved to be the Centropomidae. In Campbell et al. (2013), we also provided a critical review of the morphological evidence in favor flatfish monophyly showing that this evidence requires a careful re-examination where it concerns psettodoids. Here we present our perspective on the issues raised in Betancur-R and Ortí (2014).

  12. Comparative Cytogenetics between Two Important Songbird, Models: The Zebra Finch and the Canary

    PubMed Central

    dos Santos, Michelly da Silva; Kretschmer, Rafael; Frankl-Vilches, Carolina; Bakker, Antje; Gahr, Manfred; O´Brien, Patricia C. M.; Ferguson-Smith, Malcolm A.

    2017-01-01

    Songbird species (order Passeriformes, suborder Oscines) are important models in various experimental fields spanning behavioural genomics to neurobiology. Although the genomes of some songbird species were sequenced recently, the chromosomal organization of these species is mostly unknown. Here we focused on the two most studied songbird species in neuroscience, the zebra finch (Taeniopygia guttata) and the canary (Serinus canaria). In order to clarify these issues and also to integrate chromosome data with their assembled genomes, we used classical and molecular cytogenetics in both zebra finch and canary to define their chromosomal homology, localization of heterochromatic blocks and distribution of rDNA clusters. We confirmed the same diploid number (2n = 80) in both species, as previously reported. FISH experiments confirmed the occurrence of multiple paracentric and pericentric inversions previously found in other species of Passeriformes, providing a cytogenetic signature for this order, and corroborating data from in silico analyses. Additionally, compared to other Passeriformes, we detected differences in the zebra finch karyotype concerning the morphology of some chromosomes, in the distribution of 5S rDNA clusters, and an inversion in chromosome 1. PMID:28129381

  13. Diversity of culturable nocardioform actinomycetes from wastewater treatment plants in Spain and their role in the biodegradability of aromatic compounds.

    PubMed

    Soler, Albert; García-Hernández, Jorge; Zornoza, Andrés; Alonso, José Luis

    2017-03-06

    Currently, municipal and industrial wastewater treatment plants (WWTPs) are mainly focusing on reduction of biological oxygen demand and on the removal of nutrients. However, there are microorganisms that interfere with the process. In this environment, there is a large diversity of microorganisms that have not been studied in detail and that could provide real and practical solutions to the foaming problems. Among such microorganisms, Gram-positive actinomycete bacteria are of special interest because they are known for producing secondary metabolites as well as chemically diverse compounds and for their capacity to degrade recalcitrant pollutants. Three different media were chosen to isolate actinomycetes from 28 WWTPs in Spain. A total of 189 activated sludge samples were collected; 126 strains were isolated and identified to belong to 1 suborder, i.e. Corynebacterineae, and 7 genera, i.e. Corynebacterium, Dietzia, Gordonia, Mycobacterium, Rhodococcus, Tsukamurella and Williamsia. Furthermore, 71 strains were capable of biodegrading at least 1 aromatic product, and that 27 of them amplified for catA gene. The results of this research help us understand the complexity of the foam-forming microbial populations in Spain and it shows that WWTPs can be a good source of microorganisms that can degrade phenol or naphthalene.

  14. Penis morphology in a Burmese amber harvestman.

    PubMed

    Dunlop, Jason A; Selden, Paul A; Giribet, Gonzalo

    2016-02-01

    A unique specimen of the fossil harvestman Halitherses grimaldii Giribet and Dunlop, 2005 (Arachnida: Opiliones) from the Cretaceous (ca. 99 Ma) Burmese amber of Myanmar reveals a fully extended penis. This is the first record of a male copulatory organ of this nature preserved in amber and is of special importance due to the age of the deposit. The penis has a slender, distally flattened truncus, a spatulate heart-shaped glans and a short distal stylus, twisted at the tip. In living harvestmen, the penis yields crucial characters for their systematics. Male genital morphology in H. grimaldii appears to be unique among the wider Dyspnoi clade to which this fossil belongs. The large eyes in the fossil differ markedly from other members of the subfamily Ortholasmatinae to which H. grimaldii was originally referred. Based on recent data, it has been argued that large eyes may be plesiomorphic for Palpatores (i.e. the suborders Eupnoi and Dyspnoi), potentially rendering this character plesiomorphic for the fossil too. Thus, the unique structure of the penis seen here, and the probable lack of diaphanous teeth, present in all other extant non-acropsopilionid Dyspnoi, suggest that H. grimaldii represents a new, extinct family of large-eyed dyspnoid harvestmen, Halithersidae fam. nov.; a higher taxon in amber diagnosed here on both somatic and genital characters.

  15. Penis morphology in a Burmese amber harvestman

    NASA Astrophysics Data System (ADS)

    Dunlop, Jason A.; Selden, Paul A.; Giribet, Gonzalo

    2016-02-01

    A unique specimen of the fossil harvestman Halitherses grimaldii Giribet and Dunlop, 2005 (Arachnida: Opiliones) from the Cretaceous (ca. 99 Ma) Burmese amber of Myanmar reveals a fully extended penis. This is the first record of a male copulatory organ of this nature preserved in amber and is of special importance due to the age of the deposit. The penis has a slender, distally flattened truncus, a spatulate heart-shaped glans and a short distal stylus, twisted at the tip. In living harvestmen, the penis yields crucial characters for their systematics. Male genital morphology in H. grimaldii appears to be unique among the wider Dyspnoi clade to which this fossil belongs. The large eyes in the fossil differ markedly from other members of the subfamily Ortholasmatinae to which H. grimaldii was originally referred. Based on recent data, it has been argued that large eyes may be plesiomorphic for Palpatores (i.e. the suborders Eupnoi and Dyspnoi), potentially rendering this character plesiomorphic for the fossil too. Thus, the unique structure of the penis seen here, and the probable lack of diaphanous teeth, present in all other extant non-acropsopilionid Dyspnoi, suggest that H. grimaldii represents a new, extinct family of large-eyed dyspnoid harvestmen, Halithersidae fam. nov.; a higher taxon in amber diagnosed here on both somatic and genital characters.

  16. Masticatory muscles of the great-gray kangaroo (Macropus giganteus).

    PubMed

    Tomo, Soichiro; Tomo, Ikuko; Townsend, Grant C; Hirata, Kazuaki

    2007-04-01

    The great-gray kangaroo (Macropus giganteus) belongs to the Diprotodontia suborder (herbivorous marsupials of Australia) of the order of marsupials. We dissected the masticatory muscles in the great-gray kangaroo and classified them based on their innervation. Three (two male and one female) adult great-gray kangaroos (M. giganteus), fixed with 10% formalin, were examined. The masseter muscle of the great-gray kangaroo was classified into four layers (superficial layers 1, 2, 3, and a deep layer), all innervated by masseteric nerves. Layer 1 of the masseter muscle was well developed and the deep layer inserted into the masseteric canal. The zygomaticomandibular muscle, which belongs to both the masseter and temporalis muscles, was innervated by both the masseteric nerve and posterior deep temporal nerve, and the temporalis muscle was innervated by the anterior and posterior deep temporal nerves. The medial pterygoid muscle, which was innervated by the medial pterygoid nerve, was divided into superficial and deep portions. The lateral pterygoid muscle was divided into superior and inferior heads by the buccal nerve. We propose that the relationship of the masticatory muscles in the kangaroo has evolved by passive anterior invasion of the deep layer of the masseter by the medial pterygoid muscle via the masseteric canal, associated with the development of an anteroposterior mode of mastication.

  17. The case for DUF1220 domain dosage as a primary contributor to anthropoid brain expansion

    PubMed Central

    Keeney, Jonathon G.; Dumas, Laura; Sikela, James M.

    2014-01-01

    Here we present the hypothesis that increasing copy number (dosage) of sequences encoding DUF1220 protein domains is a major contributor to the evolutionary increase in brain size, neuron number, and cognitive capacity that is associated with the primate order. We further propose that this relationship is restricted to the anthropoid sub-order of primates, with DUF1220 copy number markedly increasing in monkeys, further in apes, and most extremely in humans where the greatest number of copies (~272 haploid copies) is found. We show that this increase closely parallels the increase in brain size and neuron number that has occurred among anthropoid primate species. We also provide evidence linking DUF1220 copy number to brain size within the human species, both in normal populations and in individuals associated with brain size pathologies (1q21-associated microcephaly and macrocephaly). While we believe these and other findings presented here strongly suggest increase in DUF1220 copy number is a key contributor to anthropoid brain expansion, the data currently available rely largely on correlative measures that, though considerable, do not yet provide direct evidence for a causal connection. Nevertheless, we believe the evidence presented is sufficient to provide the basis for a testable model which proposes that DUF1220 protein domain dosage increase is a main contributor to the increase in brain size and neuron number found among the anthropoid primate species and that is at its most extreme in human. PMID:25009482

  18. Gammaproteobacteria as essential primary symbionts in the striped shield bug, Graphosoma Lineatum (Hemiptera: Pentatomidae)

    PubMed Central

    Karamipour, Naeime; Mehrabadi, Mohammad; Fathipour, Yaghoub

    2016-01-01

    Many members of suborder Heteroptra harbor heritable symbiotic bacteria. Here we characterize the gut symbiotic bacterium in Graphosoma lineatum (Hemiptera: Pentatomidae) by using molecular phylogeny, real-time PCR analysis as well as light and electron microscopy observations. The microscopy observations revealed the presence of a large number of rod-shaped bacterial cells in the crypts. A very high prevalence (98 to 100%) of the symbiont infection was found in the insect populations that strongly supports an intimate association between these two organisms. Real-time PCR analysis also showed that the Gammaproteobacteria dominated the crypts. The sequences of 16sr RNA and groEL genes of symbiont showed high levels of similarity (93 to 95%) to Pantoea agglomeranse and Erwinia herbicola Gammaproteobacteria. Phylogenetic analyses placed G. lineatum symbiont in a well-defined branch, divergent from other stink bug bacterial symbionts. Co-evolutionary analysis showed lack of host-symbiont phylogenetic congruence. Surface sterilization of eggs resulted in increased pre-adult stage in the offspring (aposymbionts) in comparison to the normal. Also, fecundity, longevity, and adult stage were significantly decreased in the aposymbionts. Therefore, it seems that the symbiont might play a vital function in the host biology, in which host optimal development depends on the symbiont. PMID:27609055

  19. Comparison of intraspecific, interspecific and intergeneric chloroplast diversity in Cycads

    PubMed Central

    Jiang, Guo-Feng; Hinsinger, Damien Daniel; Strijk, Joeri Sergej

    2016-01-01

    Cycads are among the most threatened plant species. Increasing the availability of genomic information by adding whole chloroplast data is a fundamental step in supporting phylogenetic studies and conservation efforts. Here, we assemble a dataset encompassing three taxonomic levels in cycads, including ten genera, three species in the genus Cycas and two individuals of C. debaoensis. Repeated sequences, SSRs and variations of the chloroplast were analyzed at the intraspecific, interspecific and intergeneric scale, and using our sequence data, we reconstruct a phylogenomic tree for cycads. The chloroplast was 162,094 bp in length, with 133 genes annotated, including 87 protein-coding, 37 tRNA and 8 rRNA genes. We found 7 repeated sequences and 39 SSRs. Seven loci showed promising levels of variations for application in DNA-barcoding. The chloroplast phylogeny confirmed the division of Cycadales in two suborders, each of them being monophyletic, revealing a contradiction with the current family circumscription and its evolution. Finally, 10 intraspecific SNPs were found. Our results showed that despite the extremely restricted distribution range of C. debaoensis, using complete chloroplast data is useful not only in intraspecific studies, but also to improve our understanding of cycad evolution and in defining conservation strategies for this emblematic group. PMID:27558458

  20. Community structure variability of Uropodina mites (Acari: Mesostigmata) in nests of the common mole, Talpa europaea, in Central Europe.

    PubMed

    Napierała, Agnieszka; Mądra, Anna; Leszczyńska-Deja, Kornelia; Gwiazdowicz, Dariusz J; Gołdyn, Bartłomiej; Błoszyk, Jerzy

    2016-04-01

    Underground nests of Talpa europaea, known as the common mole, are very specific microhabitats, which are also quite often inhabited by various groups of arthropods. Mites from the suborder Uropodina (Acari: Mesostigmata) are only one of them. One could expect that mole nests that are closely located are inhabited by communities of arthropods with similar species composition and structure. However, results of empirical studies clearly show that even nests which are close to each other can be different both in terms of the species composition and abundance of Uropodina communities. So far, little is known about the factors that can cause these differences. The major aim of this study was to identify factors determining species composition, abundance, and community structure of Uropodina communities in mole nests. The study is based on material collected during a long-term investigation conducted in western parts of Poland. The results indicate that the two most important factors influencing species composition and abundance of Uropodina communities in mole nests are nest-building material and depth at which nests are located. Composition of Uropodina communities in nests of moles was also compared with that of other microhabitats (e.g. rotten wood, forest litter, soil) based on data from 4421 samples collected in Poland. Communities of this habitat prove most similar to these of open areas, especially meadows, as well as some forest types.

  1. Wolbachia supergroups A and B in natural populations of medically important filth flies (diptera: muscidae, calliphoridae, and sarcophagidae) in Thailand.

    PubMed

    Mingchay, Pichanon; Sai-Ngam, Arkhom; Phumee, Atchara; Bhakdeenuan, Payu; Lorlertthum, Kittitouch; Thavara, Usavadee; Tawatsin, Apiwat; Choochote, Wej; Siriyasatien, Padet

    2014-03-01

    Filth flies, belonging to suborder Brachycera (Family; Muscidae, Calliphoridae and Sarcophagidae), are a major cause of nuisance and able to transmit pathogens to humans and animals. These insects are distributed worldwide and their populations are increasing especially in sub-tropical and tropical areas. One strategy for controlling insects employs Wolbachia, which is a group of maternally inherited intracellular bacteria, found in many insect species. The bacteria can cause reproductive abnormalities in their hosts, such as cytoplasmic incompatibility, feminization, parthenogenesis, and male lethality. In this study we determined Wolbachia endosymbionts in natural population of medically important flies (42 females and 9 males) from several geographic regions of Thailand. Wolbachia supergroups A or B were detected in 7 of female flies using PCR specific for wsp. Sequence analysis of wsp showed variations between and within the Wolbachia supergroup. Phylogenetics demonstrated that wsp is able to diverge between Wolbachia supergroups A and B. These data should be useful in future Wolbachia-based programs of fly control.

  2. A molecular phylogeny of the Octopoda (Mollusca: Cephalopoda) evaluated in light of morphological evidence.

    PubMed

    Carlini, D B; Young, R E; Vecchione, M

    2001-12-01

    In this paper we examine the phylogenetic relationships of the Octopoda utilizing molecular sequence data from the cytochrome c oxidase subunit I (COI) gene and compare results from analyses of molecular data with classifications and phylogenies based on previous morphological studies. Partial COI sequences (657 bp, excluding primers) were obtained from 28 species representing most of the diversity in the Order Octopoda, along with a sequence from the established sister taxon to the Octopoda, Vampyroteuthis infernalis. Our results exhibit a number of basic differences from inferences based on standard morphological data. We attempt to resolve these differences based on our confidence in various morphological features. An important finding is the failure of the molecular data to support the monophyly of the Octopodidae. This family contains over 90% of the species in the Suborder Incirrata and has always been difficult to define. Statistical tests constraining Octopodidae monophyly by use of parsimony and maximum-likelihood techniques suggest that all incirrates may be derived from octopodids.

  3. Molecular evidence for multiple origins of Insectivora and for a new order of endemic African insectivore mammals

    PubMed Central

    Stanhope, Michael J.; Waddell, Victor G.; Madsen, Ole; de Jong, Wilfried; Hedges, S. Blair; Cleven, Gregory C.; Kao, Diana; Springer, Mark S.

    1998-01-01

    The traditional views regarding the mammalian order Insectivora are that the group descended from a single common ancestor and that it is comprised of the following families: Soricidae (shrews), Tenrecidae (tenrecs), Solenodontidae (solenodons), Talpidae (moles), Erinaceidae (hedgehogs and gymnures), and Chrysochloridae (golden moles). Here we present a molecular analysis that includes representatives of all six families of insectivores, as well as 37 other taxa representing marsupials, monotremes, and all but two orders of placental mammals. These data come from complete sequences of the mitochondrial 12S rRNA, tRNA-Valine, and 16S rRNA genes (2.6 kb). A wide range of different methods of phylogenetic analysis groups the tenrecs and golden moles (both endemic to Africa) in an all-African superordinal clade comprised of elephants, sirenians, hyracoids, aardvark, and elephant shrews, to the exclusion of the other four remaining families of insectivores. Statistical analyses reject the idea of a monophyletic Insectivora as well as traditional concepts of the insectivore suborder Soricomorpha. These findings are supported by sequence analyses of several nuclear genes presented here: vWF, A2AB, and α-β hemoglobin. These results require that the order Insectivora be partitioned and that the two African families (golden moles and tenrecs) be placed in a new order. The African superordinal clade now includes six orders of placental mammals. PMID:9707584

  4. Troponin-like regulation in muscle thin filaments of the mussel Crenomytilus grayanus (Bivalvia: Mytiloida).

    PubMed

    Vyatchin, Ilya G; Shevchenko, Ulyana V; Lazarev, Stanislav S; Matusovsky, Oleg S; Shelud'ko, Nikolay S

    2015-10-01

    Muscles of bivalve molluscs have double calcium regulation--myosin-linked and actin-linked. While the mechanism of myosin-linked regulation is sufficiently studied, there is still no consensus on the mechanism of actin-linked regulation. Earlier we showed a high degree of Ca2+-sensitivity of thin filaments from the adductor muscle of the mussel Crenomytilus grayanus (Mytiloida). In order to elucidate the nature of this regulation, we isolated the fraction of minor proteins from the mussel thin filaments, which confers Ca2+-sensitivity to reconstituted actomyosin-tropomyosin. Proteins of this fraction, ABP-19, ABP-20, and ABP-28, were chromatographically purified and identified. According to the results of mass spectrometry and Western blot analysis, as well as by their functional properties, these mussel actin-binding proteins appeared to correspond to the troponin components from the skeletal muscles of vertebrates (TnC, TnI and TnT). The reconstituted mussel troponin complex confers to actomyosin-tropomyosin more than 80% Ca2+-sensitivity. The in vivo molar ratio of actin/tropomyosin/troponin was calculated to be 7:1:0.5, i.e., the content of troponin in mussel thin filaments is two times lower than in thin filaments of skeletal muscles of vertebrates. These data demonstrate that troponin-like regulation found in the catch muscle of the mussel C. grayanus is present at least in two suborders of bivalves: Pectinoida and Mytiloida.

  5. The fossil record and macroevolutionary history of the beetles

    PubMed Central

    Smith, Dena M.; Marcot, Jonathan D.

    2015-01-01

    Coleoptera (beetles) is the most species-rich metazoan order, with approximately 380 000 species. To understand how they came to be such a diverse group, we compile a database of global fossil beetle occurrences to study their macroevolutionary history. Our database includes 5553 beetle occurrences from 221 fossil localities. Amber and lacustrine deposits preserve most of the beetle diversity and abundance. All four extant suborders are found in the fossil record, with 69% of all beetle families and 63% of extant beetle families preserved. Considerable focus has been placed on beetle diversification overall, however, for much of their evolutionary history it is the clade Polyphaga that is most responsible for their taxonomic richness. Polyphaga had an increase in diversification rate in the Early Cretaceous, but instead of being due to the radiation of the angiosperms, this was probably due to the first occurrences of beetle-bearing amber deposits in the record. Perhaps, most significant is that polyphagan beetles had a family-level extinction rate of zero for most of their evolutionary history, including across the Cretaceous–Palaeogene boundary. Therefore, focusing on the factors that have inhibited beetle extinction, as opposed to solely studying mechanisms that may promote speciation, should be examined as important determinants of their great diversity today. PMID:25788597

  6. Integration of remote sensing (RS) and geographic information system (GIS) techniques for change detection of the land use and land cover (LULC) for soil management in the southern Port Said region, Egypt

    NASA Astrophysics Data System (ADS)

    Hassan, Mohamed Abd El Rehim Abd El Aziz

    2014-11-01

    The monitoring of land use/land cover (LULC) changes in southern Port Said region area is very important for the planner of managements, governmental and non-governmental organizations, decision makers and the scientific community. This information is essential for planning and implementing policies to optimize the use of natural resources and accommodate development whilst minimizing the impact on the environment. To monitor these changes in the study area, two sets of satellite images (Landsat TM-5 and ETM+7) data were used with Path/Row (175/38) in date 1986 and 2006, respectively. The Landsat TM and ETM data are useful for this type of study due to its high spatial resolution, spectral resolution and low repetitive acquisition (16 days). A postclassification technique is used in this study based on hybrid classification (Unsupervised and Supervised). Each method used was assessed, and checked in field. Eight to Twelve LULC classes are recognized and mapping produced. The soils in southern Port Said area were classification in two orders for soil taxonomic units, which are Entisols and Aridisols and four sub-orders classes. The study land was evaluated into five classes from non suitable (N) to very highly suitable (S1) for some crops in the southern region of Port Said studied soils, with assess the nature of future change following construction of the international coastal road which crosses near to the study area.

  7. Meiotic Chromosome Analysis of the Giant Water Bug, Lethocerus indicus

    PubMed Central

    Wisoram, Wijit; Saengthong, Pradit; Ngernsiri, Lertluk

    2013-01-01

    The giant water bug, Lethocerus indicus (Lepeletier and Serville) (Heteroptera: Belostomatidae), a native species of Southeast Asia, is one of the largest insects belonging to suborder Heteroptera. In this study, the meiotic chromosome of L. indicus was studied in insect samples collected from Thailand, Myanmar, Loas, and Cambodia. Testicular cells stained with lacto-acetic orcein, Giemsa, DAPI, and silver nitrate were analyzed. The results revealed that the chromosome complement of L. indicus was 2n = 22A + neo-XY + 2m, which differed from that of previous reports. Each individual male contained testicular cells with three univalent patterns. The frequency of cells containing neo-XY chromosome univalent (∼5%) was a bit higher than that of cells with autosomal univalents (∼3%). Some cells (∼0.5%) had both sex chromosome univalents and a pair of autosomal univalents. None of the m-chromosome univalents were observed during prophase I. In addition, this report presents clear evidence about the existence of m-chromosomes in Belostomatidae. PMID:23895100

  8. Characterization of an Obligate Intracellular Bacterium in the Midgut Epithelium of the Bulrush Bug Chilacis typhae (Heteroptera, Lygaeidae, Artheneinae)▿

    PubMed Central

    Kuechler, Stefan Martin; Dettner, Konrad; Kehl, Siegfried

    2011-01-01

    Many members of the suborder Heteroptera have symbiotic bacteria, which are usually found extracellularly in specific sacs or tubular outgrowths of the midgut or intracellularly in mycetomes. In this study, we describe the second molecular characterization of a symbiotic bacterium in a monophagous, seed-sucking stink bug of the family Lygaeidae (sensu stricto). Chilacis typhae possesses at the end of the first section of the midgut a structure which is composed of circularly arranged, strongly enlarged midgut epithelial cells. It is filled with an intracellular endosymbiont. This “mycetocytic belt” might represent an evolutionarily intermediate stage of the usual symbiotic structures found in stink bugs. Phylogenetic analysis based on the 16S rRNA and the groEL genes showed that the bacterium belongs to the Gammaproteobacteria, and it revealed a phylogenetic relationship with a secondary bacterial endosymbiont of Cimex lectularius and free-living plant pathogens such as Pectobacterium and Dickeya. The distribution and ultrastructure of the rod-shaped Chilacis endosymbiont were studied in adults and nymph stages using fluorescence in situ hybridization (FISH) and electron microscopy. The detection of symbionts at the anterior poles of developing eggs indicates that endosymbionts are transmitted vertically. A new genus and species name, “Candidatus Rohrkolberia cinguli,” is proposed for this newly characterized clade of symbiotic bacteria. PMID:21378044

  9. Evolutionary origin of the Scombridae (tunas and mackerels): members of a paleogene adaptive radiation with 14 other pelagic fish families.

    PubMed

    Miya, Masaki; Friedman, Matt; Satoh, Takashi P; Takeshima, Hirohiko; Sado, Tetsuya; Iwasaki, Wataru; Yamanoue, Yusuke; Nakatani, Masanori; Mabuchi, Kohji; Inoue, Jun G; Poulsen, Jan Yde; Fukunaga, Tsukasa; Sato, Yukuto; Nishida, Mutsumi

    2013-01-01

    Uncertainties surrounding the evolutionary origin of the epipelagic fish family Scombridae (tunas and mackerels) are symptomatic of the difficulties in resolving suprafamilial relationships within Percomorpha, a hyperdiverse teleost radiation that contains approximately 17,000 species placed in 13 ill-defined orders and 269 families. Here we find that scombrids share a common ancestry with 14 families based on (i) bioinformatic analyses using partial mitochondrial and nuclear gene sequences from all percomorphs deposited in GenBank (10,733 sequences) and (ii) subsequent mitogenomic analysis based on 57 species from those targeted 15 families and 67 outgroup taxa. Morphological heterogeneity among these 15 families is so extraordinary that they have been placed in six different perciform suborders. However, members of the 15 families are either coastal or oceanic pelagic in their ecology with diverse modes of life, suggesting that they represent a previously undetected adaptive radiation in the pelagic realm. Time-calibrated phylogenies imply that scombrids originated from a deep-ocean ancestor and began to radiate after the end-Cretaceous when large predatory epipelagic fishes were selective victims of the Cretaceous-Paleogene mass extinction. We name this clade of open-ocean fishes containing Scombridae "Pelagia" in reference to the common habitat preference that links the 15 families.

  10. Estimating Tempo and Mode of Y Chromosome Turnover: Explaining Y Chromosome Loss With the Fragile Y Hypothesis

    PubMed Central

    Blackmon, Heath; Demuth, Jeffery P.

    2014-01-01

    Chromosomal sex determination is phylogenetically widespread, having arisen independently in many lineages. Decades of theoretical work provide predictions about sex chromosome differentiation that are well supported by observations in both XY and ZW systems. However, the phylogenetic scope of previous work gives us a limited understanding of the pace of sex chromosome gain and loss and why Y or W chromosomes are more often lost in some lineages than others, creating XO or ZO systems. To gain phylogenetic breadth we therefore assembled a database of 4724 beetle species’ karyotypes and found substantial variation in sex chromosome systems. We used the data to estimate rates of Y chromosome gain and loss across a phylogeny of 1126 taxa estimated from seven genes. Contrary to our initial expectations, we find that highly degenerated Y chromosomes of many members of the suborder Polyphaga are rarely lost, and that cases of Y chromosome loss are strongly associated with chiasmatic segregation during male meiosis. We propose the “fragile Y” hypothesis, that recurrent selection to reduce recombination between the X and Y chromosome leads to the evolution of a small pseudoautosomal region (PAR), which, in taxa that require XY chiasmata for proper segregation during meiosis, increases the probability of aneuploid gamete production, with Y chromosome loss. This hypothesis predicts that taxa that evolve achiasmatic segregation during male meiosis will rarely lose the Y chromosome. We discuss data from mammals, which are consistent with our prediction. PMID:24939995

  11. The closest relatives of cacti: insights from phylogenetic analyses of chloroplast and mitochondrial sequences with special emphasis on relationships in the tribe Anacampseroteae.

    PubMed

    Nyffeler, Reto

    2007-01-01

    Recent molecular and morphological systematic investigations revealed that the cacti are most closely related to Anacampseroteae, Portulaca and Talinum of the family Portulacaceae (ACPT clade of suborder Portulacineae). A combined analysis of ndhF, matK, and nad1 sequence data from the chloroplast and the mitochondrial genomes indicates that the tribe Anacampseroteae is the sister group of the family Cactaceae. This clade, together with Portulaca, is well characterized by the presence of axillary hairs or scales. Relationships within Anacampseroteae are characterized by a grade of five species of Grahamia s.l. from North and South America, and Grahamia australiana is found to be sister to the genera Anacampseros and Avonia. A comparison of vegetative characteristics indicates an evolutionary transition from woody subshrubs to dwarf perennial and highly succulent herbs during the diversification of Anacampseroteae. Available evidence from the present investigation as well as from previously published studies suggests that a revised classification of Portulacineae on the basis of inferred phylogenetic relationships might consist of a superfamily that includes Cactaceae and the three genera Anacampseros s.l. (including Avonia and Grahamia s.l.), Portulaca, and Talinum (including Talinella), either referred to three monogeneric families or to a paraphyletic family Portulacaceae*.

  12. Ribosomal ITS sequences allow resolution of freshwater sponge phylogeny with alignments guided by secondary structure prediction.

    PubMed

    Itskovich, Valeria; Gontcharov, Andrey; Masuda, Yoshiki; Nohno, Tsutomu; Belikov, Sergey; Efremova, Sofia; Meixner, Martin; Janussen, Dorte

    2008-12-01

    Freshwater sponges include six extant families which belong to the suborder Spongillina (Porifera). The taxonomy of freshwater sponges is problematic and their phylogeny and evolution are not well understood. Sequences of the ribosomal internal transcribed spacers (ITS1 and ITS2) of 11 species from the family Lubomirskiidae, 13 species from the family Spongillidae, and 1 species from the family Potamolepidae were obtained to study the phylogenetic relationships between endemic and cosmopolitan freshwater sponges and the evolution of sponges in Lake Baikal. The present study is the first one where ITS1 sequences were successfully aligned using verified secondary structure models and, in combination with ITS2, used to infer relationships between the freshwater sponges. Phylogenetic trees inferred using maximum likelihood, neighbor-joining, and parsimony methods and Bayesian inference revealed that the endemic family Lubomirskiidae was monophyletic. Our results do not support the monophyly of Spongillidae because Lubomirskiidae formed a robust clade with E. muelleri, and Trochospongilla latouchiana formed a robust clade with the outgroup Echinospongilla brichardi (Potamolepidae). Within the cosmopolitan family Spongillidae the genera Radiospongilla and Eunapius were found to be monophyletic, while Ephydatia muelleri was basal to the family Lubomirskiidae. The genetic distances between Lubomirskiidae species being much lower than those between Spongillidae species are indicative of their relatively recent radiation from a common ancestor. These results indicated that rDNA spacers sequences can be useful in the study of phylogenetic relationships of and the identification of species of freshwater sponges.

  13. Molecular phylogeny of land and freshwater planarians (Tricladida, Platyhelminthes): from freshwater to land and back.

    PubMed

    Alvarez-Presas, Marta; Baguñà, Jaume; Riutort, Marta

    2008-05-01

    The suborder Tricladida (phylum Platyhelminthes) comprises the well-known free-living flatworms, taxonomically grouped into three infraorders according to their ecology: Maricola (marine planarians), Paludicola (freshwater planarians), and Terricola (land planarians). Molecular analyses have demonstrated that the Paludicola are paraphyletic, the Terricola being the sister group of one of the three paludicolan families, the Dugesiidae. However, neither 18S rDNA nor COI based trees have been able to resolve the relationships among species of Terricola and Dugesiidae, particularly the monophyly of Terricola. Here, we present new molecular data including sequences of nuclear genes (18S rDNA, 28S rDNA) and a mitochondrial gene (COI) of a wider sample of dugesiid and terricolan species. The new sequences have been analyzed, together with those previously obtained, in independent and concatenated analyses using maximum likelihood and bayesian methods. The results show that, although some parts of the trees remain poorly resolved, they support a monophyletic origin for Terricola followed by a likely return of some species to freshwater habitats. Relationships within the monophyletic group of Dugesiidae are clearly resolved, and relationships among some terricolan subfamilies are also clearly established and point to the need for a thorough revision of Terricola taxonomy.

  14. Multi-locus fossil-calibrated phylogeny of Atheriniformes (Teleostei, Ovalentaria).

    PubMed

    Campanella, Daniela; Hughes, Lily C; Unmack, Peter J; Bloom, Devin D; Piller, Kyle R; Ortí, Guillermo

    2015-05-01

    Phylogenetic relationships among families within the order Atheriniformes have been difficult to resolve on the basis of morphological evidence. Molecular studies so far have been fragmentary and based on a small number taxa and loci. In this study, we provide a new phylogenetic hypothesis based on sequence data collected for eight molecular markers for a representative sample of 103 atheriniform species, covering 2/3 of the genera in this order. The phylogeny is calibrated with six carefully chosen fossil taxa to provide an explicit timeframe for the diversification of this group. Our results support the subdivision of Atheriniformes into two suborders (Atherinopsoidei and Atherinoidei), the nesting of Notocheirinae within Atherinopsidae, and the monophyly of tribe Menidiini, among others. We propose taxonomic changes for Atherinopsoidei, but a few weakly supported nodes in our phylogeny suggests that further study is necessary to support a revised taxonomy of Atherinoidei. The time-calibrated phylogeny was used to infer ancestral habitat reconstructions to explain the current distribution of marine and freshwater taxa. Based on these results, the current distribution of Atheriniformes is likely due to widespread marine dispersal along the margins of continents, infrequent trans-oceanic dispersal, and repeated invasion of freshwater habitats. This conclusion is supported by post-Gondwanan divergence times among families within the order, and a high probability of a marine ancestral habitat.

  15. Chemical ecology of oribatid mites III. Chemical composition of oil gland exudates from two oribatid mites, Trhypochthoniellus sp. and Trhypochthonius japonicus (Acari: Trhypochthoniidae).

    PubMed

    Sakata, Tomoyo; Shimano, Satoshi; Kuwahara, Yasumasa

    2003-01-01

    The composition of oil gland exudates from two oribatid mites, Trhypochthoniellus sp. and Trhypochthonius japonicus, was studied with reference to the related species Trhypochthoniellus crassus. Trhypochthoniellus sp. contained a mixture of seven compounds; (Z,Z)-6,9-heptadecadiene, geranial, 3-hydroxybenzene-1,2-dicarbaldehyde (gamma-acaridial), neryl formate, neral, (Z)-8-heptadecene and geranyl formate in decreasing order of abundance. The profile of the components from T. japonicus consisted of two types depending on the locality of sampling with unknown reason; one possessing a mixture of eight compounds [(Z,E)-farnesal, gamma-acaridial, (Z,Z)-6,9-heptadecadiene, (E,E)-farnesal, (Z)-8-heptadecene and geranial in decreasing order] together with two unknown compounds, and the other composed of the same set of compounds together with 2-hydroxy-6-methylbenzaldehyde as the most abundant component. Relative abundance among common components was consistent between the two types of T. japonicus. Profiles of components differed among three species including T. crasus. The phylogenetic relationship between Oribatida and Astigmata was discussed based on secretory compounds commonly distributed between these two suborders.

  16. Structural Analysis of a Repetitive Protein Sequence Motif in Strepsirrhine Primate Amelogenin

    PubMed Central

    Bromley, Keith M.; Hacia, Joseph G.; Bromage, Timothy G.; Snead, Malcolm L.; Moradian-Oldak, Janet; Paine, Michael L.

    2011-01-01

    Strepsirrhines are members of a primate suborder that has a distinctive set of features associated with the development of the dentition. Amelogenin (AMEL), the better known of the enamel matrix proteins, forms 90% of the secreted organic matrix during amelogenesis. Although AMEL has been sequenced in numerous mammalian lineages, the only reported strepsirrhine AMEL sequences are those of the ring-tailed lemur and galago, which contain a set of additional proline-rich tandem repeats absent in all other primates species analyzed to date, but present in some non-primate mammals. Here, we first determined that these repeats are present in AMEL from three additional lemur species and thus are likely to be widespread throughout this group. To evaluate the functional relevance of these repeats in strepsirrhines, we engineered a mutated murine amelogenin sequence containing a similar proline-rich sequence to that of Lemur catta. In the monomeric form, the MQP insertions had no influence on the secondary structure or refolding properties, whereas in the assembled form, the insertions increased the hydrodynamic radii. We speculate that increased AMEL nanosphere size may influence enamel formation in strepsirrhine primates. PMID:21437261

  17. The evolution of polar fish hemoglobin: a phylogenetic analysis of the ancestral amino acid residues linked to the root effect.

    PubMed

    Verde, Cinzia; Parisi, Elio; di Prisco, Guido

    2003-01-01

    Originating from a benthic ancestor, the suborder Notothenioidei (the dominant fish fauna component of the Antarctic sea) underwent a remarkable radiation, which led notothenioids to fill several niches. The ecological importance of notothenioids in Antarctica and their biochemical adaptations have prompted great efforts to study their physiology and phylogeny, with special attention to the evolutionary adaptation of the oxygen-transport system. We herewith report the evolutionary history of alpha- and beta-globins under the assumption of the molecular clock hypothesis as a basis for reconstructing the phylogenetic relationships among species. These studies have been extended to fish species of other latitudes, including the Arctic region. The northern and southern polar oceans have very different characteristics; indeed, in many respects the Antarctic and Arctic ichthyofaunas are more dissimilar than similar. Our results show that the inferred phylogeny of Arctic and Antarctic globins is different. Taking advantage of the wealth of information collected on structure and function of hemoglobins, we have attempted to investigate the evolutionary history of an important physiological feature in fish, the Root effect. The results suggest that the amino acid residues reported to play a key role in the Root effect may be regarded as ancestor characters, but the lack of this effect in extant species can hardly be associated with the presence of synapomorphies.

  18. A molecular phylogeny of Hemiptera inferred from mitochondrial genome sequences.

    PubMed

    Song, Nan; Liang, Ai-Ping; Bu, Cui-Ping

    2012-01-01

    Classically, Hemiptera is comprised of two suborders: Homoptera and Heteroptera. Homoptera includes Cicadomorpha, Fulgoromorpha and Sternorrhyncha. However, according to previous molecular phylogenetic studies based on 18S rDNA, Fulgoromorpha has a closer relationship to Heteroptera than to other hemipterans, leaving Homoptera as paraphyletic. Therefore, the position of Fulgoromorpha is important for studying phylogenetic structure of Hemiptera. We inferred the evolutionary affiliations of twenty-five superfamilies of Hemiptera using mitochondrial protein-coding genes and rRNAs. We sequenced three mitogenomes, from Pyrops candelaria, Lycorma delicatula and Ricania marginalis, representing two additional families in Fulgoromorpha. Pyrops and Lycorma are representatives of an additional major family Fulgoridae in Fulgoromorpha, whereas Ricania is a second representative of the highly derived clade Ricaniidae. The organization and size of these mitogenomes are similar to those of the sequenced fulgoroid species. Our consensus phylogeny of Hemiptera largely supported the relationships (((Fulgoromorpha,Sternorrhyncha),Cicadomorpha),Heteroptera), and thus supported the classic phylogeny of Hemiptera. Selection of optimal evolutionary models (exclusion and inclusion of two rRNA genes or of third codon positions of protein-coding genes) demonstrated that rapidly evolving and saturated sites should be removed from the analyses.

  19. Energetic costs of protein synthesis do not differ between red- and white-blooded Antarctic notothenioid fishes.

    PubMed

    Lewis, Johanne M; Grove, Theresa J; O'Brien, Kristin M

    2015-09-01

    Antarctic icefishes (Family Channichthyidae) within the suborder Notothenioidei lack the oxygen-binding protein hemoglobin (Hb), and six of the 16 species of icefishes lack myoglobin (Mb) in heart ventricle. As iron-centered proteins, Hb and Mb can promote the formation of reactive oxygen species (ROS) that damage biological macromolecules. Consistent with this, our previous studies have shown that icefishes have lower levels of oxidized proteins and lipids in oxidative muscle compared to red-blooded notothenioids. Because oxidized proteins are usually degraded by the 20S proteasome and must be resynthesized, we hypothesized that rates of protein synthesis would be lower in icefishes compared to red-blooded notothenioids, thereby reducing the energetic costs of protein synthesis and conferring a benefit to the loss of Hb and Mb. Rates of protein synthesis were quantified in hearts, and the fraction of oxygen consumption devoted to protein synthesis was measured in isolated hepatocytes and cardiomyocytes of notothenioids differing in the expression of Hb and cardiac Mb. Neither rates of protein synthesis nor the energetic costs of protein synthesis differed among species, suggesting that red-blooded species do not degrade and replace oxidatively modified proteins at a higher rate compared to icefishes but rather, persist with higher levels of oxidized proteins.

  20. Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Baleen whale phylogeny and a past extensive radiation event revealed by SINE insertion analysis.

    PubMed

    Nikaido, Masato; Hamilton, Healy; Makino, Hitomi; Sasaki, Takeshi; Takahashi, Kazuhiko; Goto, Mutsuo; Kanda, Naohisa; Pastene, Luis A; Okada, Norihiro

    2006-05-01

    Baleen whales (suborder Mysticeti) comprise 11 extant species that are classified into four families. Although several phylogenetic hypotheses about these taxa have been proposed, their phylogenetic relationships remain confused. We addressed this problem using short interspersed repetitive element (SINE) insertion data, which now are regarded as almost ideal shared, derived characters at the molecular level. We reconstructed the phylogenetic relationships of baleen whales by characterizing 36 informative SINE loci. One of the intriguing conclusions is that balaenopterids and eschrichtiids radiated very rapidly during a very short evolutionary period. During this period, speciation occurred in balaenopterids and eschrichtiids while newly inserted SINE loci remains polymorphic. Later on, these SINEs were sorted incompletely into each lineage. Thus, there are now inconsistencies among species regarding the presence or absence of a given SINE. This is in sharp contrast to the phylogeny of toothed whales, for which no SINE inconsistencies have been found. Furthermore, we found monophyletic groupings between humpback and fin whales as well as between (sei+Bryde's) whales and blue whales, both of which have not previously been recognized. The comprehensive SINE insertion data, together with the mitochondrial DNA phylogeny that was recently completed (Sasaki, T., M. Nikaido, H. Healy et al. 2005. Mitochondrial phylogenetics and evolution of mysticete whales. Syst. Biol. 56:77-90; Rychel, A. L., T. W. Reeder, and A. Berta. 2004. Phylogeny of mysticete whales based on mitochondrial and nuclear data. Mol. Phylogenet. Evol. 32:892-901), provide a nearly complete picture of the evolutionary history of baleen whales.

  1. Use of comparative genomics to develop EST-SSRs for red drum (Sciaenops ocellatus).

    PubMed

    Hollenbeck, Christopher M; Portnoy, David S; Gold, John R

    2012-12-01

    Microsatellites physically linked to expressed sequence tags (EST-SSRs) are an important resource for linkage mapping and comparative genomics, and data mining in publicly available EST databases is a common strategy for EST-SSR discovery. At present, many species lack species-specific EST sequence data needed for the efficient characterization of EST-SSRs. This paper describes the discovery and development of EST-SSRs for red drum (Sciaenops ocellatus), an estuarine-dependent sciaenid species of economic importance in the USA and elsewhere, using a phylogenetically informed, comparative genomics approach to primer design. The approach entailed comparing existing genomic resources from species closely allied phylogenetically to red drum, with resources from more distantly related outgroup species. By taking into account the degree to which flanking regions are conserved across taxa, the efficiency of PCR primer design was increased greatly. The amplification success rate for primers designed for red drum was 100 % when using EST libraries from confamilial species and 92 % when using an EST library from a species in the same suborder. The primers developed also amplified EST-SSRs in a wide range of perciform fishes, suggesting potential use in comparative genomics. This study demonstrates that EST-SSRs can be efficiently developed for an organism when limited species-specific data are available by exploiting genomic resources from well-studied species, even those at extended phylogenetic distances.

  2. Mitochondrial and nuclear genes suggest that stony corals are monophyletic but most families of stony corals are not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria).

    PubMed

    Fukami, Hironobu; Chen, Chaolun Allen; Budd, Ann F; Collins, Allen; Wallace, Carden; Chuang, Yao-Yang; Chen, Chienhsun; Dai, Chang-Feng; Iwao, Kenji; Sheppard, Charles; Knowlton, Nancy

    2008-09-16

    Modern hard corals (Class Hexacorallia; Order Scleractinia) are widely studied because of their fundamental role in reef building and their superb fossil record extending back to the Triassic. Nevertheless, interpretations of their evolutionary relationships have been in flux for over a decade. Recent analyses undermine the legitimacy of traditional suborders, families and genera, and suggest that a non-skeletal sister clade (Order Corallimorpharia) might be imbedded within the stony corals. However, these studies either sampled a relatively limited array of taxa or assembled trees from heterogeneous data sets. Here we provide a more comprehensive analysis of Scleractinia (127 species, 75 genera, 17 families) and various outgroups, based on two mitochondrial genes (cytochrome oxidase I, cytochrome b), with analyses of nuclear genes (ss-tubulin, ribosomal DNA) of a subset of taxa to test unexpected relationships. Eleven of 16 families were found to be polyphyletic. Strikingly, over one third of all families as conventionally defined contain representatives from the highly divergent "robust" and "complex" clades. However, the recent suggestion that corallimorpharians are true corals that have lost their skeletons was not upheld. Relationships were supported not only by mitochondrial and nuclear genes, but also often by morphological characters which had been ignored or never noted previously. The concordance of molecular characters and more carefully examined morphological characters suggests a future of greater taxonomic stability, as well as the potential to trace the evolutionary history of this ecologically important group using fossils.

  3. Is the switch to an ectomycorrhizal state an evolutionary key innovation in mushroom-forming fungi? A case study in the Tricholomatineae (Agaricales).

    PubMed

    Sánchez-García, Marisol; Matheny, Patrick Brandon

    2017-01-01

    Although fungi are one of the most diverse groups of organisms, little is known about the processes that shape their high taxonomic diversity. This study focuses on evolution of ectomycorrhizal (ECM) mushroom-forming fungi, symbiotic associates of many trees and shrubs, in the suborder Tricholomatineae of the Agaricales. We used the BiSSE model and BAMM to test the hypothesis that the ECM habit represents an evolutionary key innovation that allowed the colonization of new niches followed by an increase in diversification rate. Ancestral state reconstruction (ASR) supports the ancestor of the Tricholomatineae as non-ECM. We detected two diversification rate increases in the genus Tricholoma and the Rhodopolioid clade of the genus Entoloma. However, no increases in diversification were detected in the four other ECM clades of Tricholomatineae. We suggest that diversification of Tricholoma was not only due to the evolution of the ECM lifestyle, but also to the expansion and dominance of its main hosts and ability to associate with a variety of hosts. Diversification in the Rhodopolioid clade could be due to the unique combination of spore morphology and ECM habit. The spore morphology may represent an exaptation that aided spore dispersal and colonization. This is the first study to investigate rate shifts across a phylogeny that contains both non-ECM and ECM lineages.

  4. Cross-reactivity of anti-yellowtail thymic lymphocyte monoclonal antibody (YeT-2) with lymphocytes from other fish species.

    PubMed

    Nishimura, H; Ikemoto, M; Kawai, K; Kusuda, R

    1997-03-01

    The monoclonal antibody YeT-2, generated in mice hyper-immunized with thymic lymphocytes of the yellowtail, Seriola quinqueradiata, reacts with the major population of peripheral blood lymphocytes, which might be putative T cells. In this study, we examined the cross-reactivity of YeT-2 with lymphocytes from various fish species. Flow cytometric analysis showed that YeT-2 reacts with 69.8% lymphocytes in the thymus, 89.7% in the peripheral blood, 87.5% in the spleen, and 59.7% in the head-kidney. Among the six fish species examined, only the red sea bream, Pagrus major, which is included in the same suborder Percoidei with the yellowtail, showed the presence of YeT-2 positive cells. Electron microscopic studies revealed that YeT-2 positive cells in the peripheral blood of the red sea bream were lymphocytes or unidentified leucocytes. Thymic lymphocytes of the red sea bream were also immunocytochemically stained with YeT-2. The molecular weight of the YeT-2 cross-reacting antigen on blood cells from the red sea bream was identical with that from the yellowtail, which was identified at approximately 115 kDa. These results suggest that the monoclonal antibody YeT-2 recognizes a conserved antigen on lymphocytes common to the red sea bream and yellowtail.

  5. Bozasella gracilis n. sp. (Ciliophora, Entodiniomorphida) from Asian elephant and phylogenetic analysis of entodiniomorphids and vestibuliferids.

    PubMed

    Ito, Akira; Ishihara, Miki; Imai, Soichi

    2014-04-01

    Bozasella gracilis n. sp. in the order Entodiniomorphida was found in fecal samples of an Asian elephant kept in a zoo. The ciliate has general and infraciliary similarities to the families Ophryoscolecidae and Cycloposthiidae. Phylogenetic trees were inferred from 18S rRNA gene sequences of B. gracilis, 45 entodiniomorphids, 10 vestibuliferids, 5 macropodiniids, and an outgroup, using maximum likelihood, Bayesian inference, and neighbor joining analyses. Of them, there were 32 new sequences; 26 entodiniomorphid species in the genera, Bozasella, Triplumaria, Gassovskiella, Ditoxum, Spirodinium, Triadinium, Tetratoxum, Pseudoentodinium, Ochoterenaia, Circodinium, Blepharocorys, Sulcoarcus, Didesmis, Alloiozona, Blepharoconus, Hemiprorodon, and Prorodonopsis, and 6 vestibuliferid species in the genera, Buxtonella, Balantidium, Helicozoster, Latteuria, and Paraisotricha. Thirty additional sequences were retrieved from the GenBank database. Phylogenetic trees revealed non-monophylies of the orders Entodiniomorphida and Vestibuliferida, the suborders Entodiniomorphina and Blepharocorythina, and the families Cycloposthiidae and Paraisotrichidae. Bozasella gracilis was sister to Triplumaria. In addition, to avoid homonymy, we propose Gilchristinidae nom. nov., Gilchristina nom. nov. and Gilchristina artemis (Ito, Van Hoven, Miyazaki & Imai, 2006) comb. nov.

  6. Biodiversity, Anti-Trypanosomal Activity Screening, and Metabolomic Profiling of Actinomycetes Isolated from Mediterranean Sponges

    PubMed Central

    Cheng, Cheng; MacIntyre, Lynsey; Abdelmohsen, Usama Ramadan; Horn, Hannes; Polymenakou, Paraskevi N.; Edrada-Ebel, RuAngelie; Hentschel, Ute

    2015-01-01

    Marine sponge–associated actinomycetes are considered as promising sources for the discovery of novel biologically active compounds. In the present study, a total of 64 actinomycetes were isolated from 12 different marine sponge species that had been collected offshore the islands of Milos and Crete, Greece, eastern Mediterranean. The isolates were affiliated to 23 genera representing 8 different suborders based on nearly full length 16S rRNA gene sequencing. Four putatively novel species belonging to genera Geodermatophilus, Microlunatus, Rhodococcus and Actinomycetospora were identified based on a 16S rRNA gene sequence similarity of < 98.5% to currently described strains. Eight actinomycete isolates showed bioactivities against Trypanosma brucei brucei TC221 with half maximal inhibitory concentration (IC50) values <20 μg/mL. Thirty four isolates from the Milos collection and 12 isolates from the Crete collection were subjected to metabolomic analysis using high resolution LC-MS and NMR for dereplication purposes. Two isolates belonging to the genera Streptomyces (SBT348) and Micromonospora (SBT687) were prioritized based on their distinct chemistry profiles as well as their anti-trypanosomal activities. These findings demonstrated the feasibility and efficacy of utilizing metabolomics tools to prioritize chemically unique strains from microorganism collections and further highlight sponges as rich source for novel and bioactive actinomycetes. PMID:26407167

  7. Brucella ceti and Brucellosis in Cetaceans

    PubMed Central

    Guzmán-Verri, Caterina; González-Barrientos, Rocío; Hernández-Mora, Gabriela; Morales, Juan-Alberto; Baquero-Calvo, Elías; Chaves-Olarte, Esteban; Moreno, Edgardo

    2012-01-01

    Since the first case of brucellosis detected in a dolphin aborted fetus, an increasing number of Brucella ceti isolates has been reported in members of the two suborders of cetaceans: Mysticeti and Odontoceti. Serological surveys have shown that cetacean brucellosis may be distributed worldwide in the oceans. Although all B. ceti isolates have been included within the same species, three different groups have been recognized according to their preferred host, bacteriological properties, and distinct genetic traits: B. ceti dolphin type, B. ceti porpoise type, and B. ceti human type. It seems that B. ceti porpoise type is more closely related to B. ceti human isolates and B. pinnipedialis group, while B. ceti dolphin type seems ancestral to them. Based on comparative phylogenetic analysis, it is feasible that the B. ceti ancestor radiated in a terrestrial artiodactyl host close to the Raoellidae family about 58 million years ago. The more likely mode of transmission of B. ceti seems to be through sexual intercourse, maternal feeding, aborted fetuses, placental tissues, vertical transmission from mother to the fetus or through fish or helminth reservoirs. The B. ceti dolphin and porpoise types seem to display variable virulence in land animal models and low infectivity for humans. However, brucellosis in some dolphins and porpoises has been demonstrated to be a severe chronic disease, displaying significant clinical and pathological signs related to abortions, male infertility, neurobrucellosis, cardiopathies, bone and skin lesions, strandings, and death. PMID:22919595

  8. Rearrangement of mitochondrial tRNA genes in flat bugs (Hemiptera: Aradidae)

    PubMed Central

    Song, Fan; Li, Hu; Shao, Renfu; Shi, Aimin; Bai, Xiaoshuan; Zheng, Xiaorong; Heiss, Ernst; Cai, Wanzhi

    2016-01-01

    The typical insect mitochondrial (mt) genome organization, which contains a single chromosome with 37 genes, was found in the infraorder Pentatomomorpha (suborder Heteroptera). The arrangement of mt genes in these true bugs is usually the same as the ancestral mt gene arrangement of insects. Rearrangement of transfer RNA (tRNA) genes, however, has been found in two subfamilies of flat bugs (Mezirinae and Calisiinae, family Aradidae). In this study, we sequenced the complete mt genomes of four species from three other subfamilies (Aradinae, Carventinae and Aneurinae). We found tRNA gene rearrangement in all of these four species. All of the rearranged tRNA genes are located between the mitochondrial control region and cox1, indicating this region as a hotspot for gene rearrangement in flat bugs; the rearrangement is likely caused by events of tandem duplication and random deletion of genes. Furthermore, our phylogenetic and dating analyses indicated that the swap of positions between trnQ and trnI occurred ~162 million years ago (MYA) in the most recent common ancestor of the five subfamilies of flat bugs investigated to date, whereas the swap of positions between trnC and trnW occurred later in the lineage leading to Calisiinae, and the translocation of trnC and trnY occurred later than 134 MYA in the lineage leading to Aradinae. PMID:27180804

  9. Antarctic teleost immunoglobulins: more extreme, more interesting.

    PubMed

    Coscia, Maria Rosaria; Varriale, Sonia; Giacomelli, Stefano; Oreste, Umberto

    2011-11-01

    We have investigated the immunoglobulin molecule and the genes encoding it in teleosts living in the Antarctic seas at the constant temperature of -1.86 °C. The majority of Antarctic teleosts belong to the suborder Notothenioidei (Perciformes), which includes only a few non-Antarctic species. Twenty-one Antarctic and two non-Antarctic Notothenioid species were included in our studies. We sequenced immunoglobulin light chains in two species and μ heavy chains, partially or totally, in twenty species. In the case of heavy chain, genomic DNA and the cDNA encoding the secreted and the membrane form were analyzed. From one species, Trematomus bernacchii, a spleen cDNA library was constructed to evaluate the diversity of VH gene segments. T. bernacchii IgM, purified from the serum and bile, was characterized. Homology Modelling and Molecular Dynamics were used to determine the molecular structure of T. bernacchii and Chionodraco hamatus immunoglobulin domains. This paper sums up the previous results and broadens them with the addition of unpublished data.

  10. Germline viral “fossils” guide in silico reconstruction of a mid-Cenozoic era marsupial adeno-associated virus

    PubMed Central

    Smith, Richard H.; Hallwirth, Claus V.; Westerman, Michael; Hetherington, Nicola A.; Tseng, Yu-Shan; Cecchini, Sylvain; Virag, Tamas; Ziegler, Mona-Larissa; Rogozin, Igor B.; Koonin, Eugene V.; Agbandje-McKenna, Mavis; Kotin, Robert M.; Alexander, Ian E.

    2016-01-01

    Germline endogenous viral elements (EVEs) genetically preserve viral nucleotide sequences useful to the study of viral evolution, gene mutation, and the phylogenetic relationships among host organisms. Here, we describe a lineage-specific, adeno-associated virus (AAV)-derived endogenous viral element (mAAV-EVE1) found within the germline of numerous closely related marsupial species. Molecular screening of a marsupial DNA panel indicated that mAAV-EVE1 occurs specifically within the marsupial suborder Macropodiformes (present-day kangaroos, wallabies, and related macropodoids), to the exclusion of other Diprotodontian lineages. Orthologous mAAV-EVE1 locus sequences from sixteen macropodoid species, representing a speciation history spanning an estimated 30 million years, facilitated compilation of an inferred ancestral sequence that recapitulates the genome of an ancient marsupial AAV that circulated among Australian metatherian fauna sometime during the late Eocene to early Oligocene. In silico gene reconstruction and molecular modelling indicate remarkable conservation of viral structure over a geologic timescale. Characterisation of AAV-EVE loci among disparate species affords insight into AAV evolution and, in the case of macropodoid species, may offer an additional genetic basis for assignment of phylogenetic relationships among the Macropodoidea. From an applied perspective, the identified AAV “fossils” provide novel capsid sequences for use in translational research and clinical applications. PMID:27377618

  11. 187-gene phylogeny of protozoan phylum Amoebozoa reveals a new class (Cutosea) of deep-branching, ultrastructurally unique, enveloped marine Lobosa and clarifies amoeba evolution.

    PubMed

    Cavalier-Smith, Thomas; Chao, Ema E; Lewis, Rhodri

    2016-06-01

    Monophyly of protozoan phylum Amoebozoa, and subdivision into subphyla Conosa and Lobosa each with different cytoskeletons, are well established. However early diversification of non-ciliate lobose amoebae (Lobosa) is poorly understood. To clarify it we used recently available transcriptomes to construct a 187-gene amoebozoan tree for 30 species, the most comprehensive yet. This robustly places new genus Atrichosa (formerly lumped with Trichosphaerium) within lobosan class Tubulinea, not Discosea as previously supposed. We identified an earliest diverging lobosan clade comprising marine amoebae armoured by porose scaliform cell-envelopes, here made a novel class Cutosea with two pseudopodially distinct new families. Cutosea comprise Sapocribrum, ATCC PRA-29 misidentified as 'Pessonella', plus from other evidence Squamamoeba. We confirm that Acanthamoeba and ATCC 50982 misidentified as Stereomyxa ramosa are closely related. Discosea have a strongly supported major subclade comprising Thecamoebida plus Glycostylida (suborders Dactylopodina, Stygamoebina; Vannellina) phylogenetically distinct from Centramoebida. Stygamoeba is sister to Dactylopodina. Himatismenida are either sister to Centramoebida or deeper branching. Discosea usually appear holophyletic (rarely paraphyletic). Paramoeba transcriptomes include prokinetoplastid Perkinsela-like endosymbiont sequences. Cunea, misidentified as Mayorella, is closer to Paramoeba than Vexillifera within holophyletic Dactylopodina. Taxon-rich site-heterogeneous rDNA trees confirm cutosan distinctiveness, allow improved conosan taxonomy, and reveal previous dictyostelid tree misrooting.

  12. Paracercomonas kinetid ultrastructure, origins of the body plan of Cercomonadida, and cytoskeleton evolution in Cercozoa.

    PubMed

    Cavalier-Smith, Thomas; Karpov, Sergey A

    2012-01-01

    Serial section reconstruction shows that kinetid ultrastructure in two genetically divergent Paracercomonas (P. virgaria, P. metabolica) is basically similar, differing somewhat from clade A cercomonads. Paracercomonas (Paracercomonadidae fam. n.) have a posterior root (dp1) attached to the posterior centriole, unlike Cercomonadidae (here revised to include only Eocercomonas, Cercomonas, Filomonas gen. n., and Neocercomonas), which belong in clade A (new suborder Cercomonadina) with Cavernomonas (Cavernomonadidae fam. n.). Whether dp1 is serially homologous to anterior root da is unclear. The common ancestor of Cercomonadida probably had five microtubular roots, two fibrillar microtubule-nucleating centres generating microtubular cones, and striated connectors between obtusely angled centrioles. Our new data leave the question of holophyly versus polyphyly of Cercomonadida unresolved, but clarify cercozoan root diversity and homologies. Ventral root vp1 is throughout Cercozoa; vp2 might be restricted to the new superclass Ventrifilosa plus Sarcomonadea. Though cercozoan microtubular arrangements differ substantially from others within the kingdom Chromista, the microtubular root numbering system used for other chromists and Plantae is applicable to them; in doing this we found that the single anterior root of excavates (probably ancestral to Chromista, Plantae and unikonts) and Euglenozoa corresponds with R3 (not R4 as previously thought) of corticate eukaryotes (Chromista plus Plantae).

  13. Molecular phylogeny, scale evolution and taxonomy of centrohelid heliozoa.

    PubMed

    Cavalier-Smith, Thomas; von der Heyden, Sophie

    2007-09-01

    Heliozoa are ubiquitous, unicellular phagotrophs with slender radiating axopodia for trapping prey. We sequenced 18S rRNA genes from 35 cultured centrohelid heliozoa (18 studied by electron microscopy) and 28 environmental libraries (18 freshwater, 10 marine), yielding 97 new sequences, this exceeding described species. Phylogenetic analyses show two major groups and that ancestral centrohelids probably had inner plate-like tangential and distinct outer radial silica scales, the latter diverging early into contrasting scale types seen in extant Pterocystis/Choanocystis and Acanthocystis/Raphidiophryidae. Scales were lost at least thrice. Pterocystis is paraphyletic, as was the classical family Acanthocystidae; Heterophrys was polyphyletic. Using scale morphology and rRNA sequences, we establish new families Pterocystidae (Pterocystis, Raineriophrys, Chlamydaster), Marophryidae (type Marophrys (Heterophrys) marina gen. et comb. nov.) and Choanocystidae, new suborders Pterocystina (Pterocystidae, Choanocystidae, Heterophryidae) and Acanthocystina (Acanthocystidae, Raphidiophryidae, Marophryidae), and ten new Pterocystis, Acanthocystis and Choanocystis species. Most clades are exclusively freshwater or exclusively marine; evolutionary transitions between these habitats have been rare.

  14. Comparative analysis of the course of the facial and transverse facial arteries in selected ruminant species.

    PubMed

    Zdun, Maciej; Frąckowiak, Hieronim; Kowalczyk, Karolina; Maryniak, Hieronim; Kiełtyka-Kurc, Agata

    2014-05-01

    The paper describes variations in patterns of origin from the main arteries as well as of branching and course demonstrated on the basis of selected facial arteries in several species of ruminants. The studies included 35 species of 27 genera, 9 subfamilies of animals belonging to families of Bovidae, Cervidae, Giraffidae and Moschidae from the suborder of Ruminantia, including species maintained by humans. Altogether, 435 preparations of head arteries were studied. Arteries of the examined animals were filled with acetone-dissolved stained vinyl superchloride or stained latex LBS3060. The facial artery was found to originate from the main arteries of the head in three different manners. In species devoid of facial arteries, the presence of a pronounced transverse facial artery could be demonstrated. Division of the animals into large and small ruminants, generally accepted by authors of animal anatomy textbooks, was found to be oversimplified and lacking in universal character, as to the patterns of origin and course of the facial artery and the transverse facial artery.

  15. Cephalic arterial pattern in New World edentates and Old World pangolins with special reference to their phylogenetic relationships and taxonomy.

    PubMed

    Bugge, J

    1979-01-01

    The cephalic arterial pattern in edentates and pangolins is described on the basis of 9 corrosion specimens, representing all the classical superfamilies, with special reference to their phylogenetic relationship and taxonomy. In this respect, the importance of the manner in which the external carotid artery system annexes the stepedial area of supply and of the course of the internal carotid artery in relation to the tympanic cavity is emphasized. The investigation does not indicate any special relationship between the New World edentates and the Old World pangolins, whereas the marked difference in the course of the internal carotid artery in recent edentates stresses the independent development of the South American anteaters compared with that of the two other edentate groups (armadillos and tree sloths). Most probably the edentates were divided very early into two main lines which have evolved independently since the early Tertiary, i.e. one for the anteaters and one for the tree sloths and armadillos, indicating a probable subdivision of the true edentates into two suborders. This subdivision is markedly different from the classical two-fold division of the edentates.

  16. Towards a phylogenetic classification of Leptothecata (Cnidaria, Hydrozoa).

    PubMed

    Maronna, Maximiliano M; Miranda, Thaís P; Peña Cantero, Álvaro L; Barbeitos, Marcos S; Marques, Antonio C

    2016-01-29

    Leptothecata are hydrozoans whose hydranths are covered by perisarc and gonophores and whose medusae bear gonads on their radial canals. They develop complex polypoid colonies and exhibit considerable morphological variation among species with respect to growth, defensive structures and mode of development. For instance, several lineages within this order have lost the medusa stage. Depending on the author, traditional taxonomy in hydrozoans may be either polyp- or medusa-oriented. Therefore, the absence of the latter stage in some lineages may lead to very different classification schemes. Molecular data have proved useful in elucidating this taxonomic challenge. We analyzed a super matrix of new and published rRNA gene sequences (16S, 18S and 28S), employing newly proposed methods to measure branch support and improve phylogenetic signal. Our analysis recovered new clades not recognized by traditional taxonomy and corroborated some recently proposed taxa. We offer a thorough taxonomic revision of the Leptothecata, erecting new orders, suborders, infraorders and families. We also discuss the origination and diversification dynamics of the group from a macroevolutionary perspective.

  17. Estimating tempo and mode of Y chromosome turnover: explaining Y chromosome loss with the fragile Y hypothesis.

    PubMed

    Blackmon, Heath; Demuth, Jeffery P

    2014-06-01

    Chromosomal sex determination is phylogenetically widespread, having arisen independently in many lineages. Decades of theoretical work provide predictions about sex chromosome differentiation that are well supported by observations in both XY and ZW systems. However, the phylogenetic scope of previous work gives us a limited understanding of the pace of sex chromosome gain and loss and why Y or W chromosomes are more often lost in some lineages than others, creating XO or ZO systems. To gain phylogenetic breadth we therefore assembled a database of 4724 beetle species' karyotypes and found substantial variation in sex chromosome systems. We used the data to estimate rates of Y chromosome gain and loss across a phylogeny of 1126 taxa estimated from seven genes. Contrary to our initial expectations, we find that highly degenerated Y chromosomes of many members of the suborder Polyphaga are rarely lost, and that cases of Y chromosome loss are strongly associated with chiasmatic segregation during male meiosis. We propose the "fragile Y" hypothesis, that recurrent selection to reduce recombination between the X and Y chromosome leads to the evolution of a small pseudoautosomal region (PAR), which, in taxa that require XY chiasmata for proper segregation during meiosis, increases the probability of aneuploid gamete production, with Y chromosome loss. This hypothesis predicts that taxa that evolve achiasmatic segregation during male meiosis will rarely lose the Y chromosome. We discuss data from mammals, which are consistent with our prediction.

  18. DNA Barcodes for Nearctic Auchenorrhyncha (Insecta: Hemiptera)

    PubMed Central

    Foottit, Robert G.; Maw, Eric; Hebert, P. D. N.

    2014-01-01

    Background Many studies have shown the suitability of sequence variation in the 5′ region of the mitochondrial cytochrome c oxidase I (COI) gene as a DNA barcode for the identification of species in a wide range of animal groups. We examined 471 species in 147 genera of Hemiptera: Auchenorrhyncha drawn from specimens in the Canadian National Collection of Insects to assess the effectiveness of DNA barcoding in this group. Methodology/Principal Findings Analysis of the COI gene revealed less than 2% intra-specific divergence in 93% of the taxa examined, while minimum interspecific distances exceeded 2% in 70% of congeneric species pairs. Although most species are characterized by a distinct sequence cluster, sequences for members of many groups of closely related species either shared sequences or showed close similarity, with 25% of species separated from their nearest neighbor by less than 1%. Conclusions/Significance This study, although preliminary, provides DNA barcodes for about 8% of the species of this hemipteran suborder found in North America north of Mexico. Barcodes can enable the identification of many species of Auchenorrhyncha, but members of some species groups cannot be discriminated. Future use of DNA barcodes in regulatory, pest management, and environmental applications will be possible as the barcode library for Auchenorrhyncha expands to include more species and broader geographic coverage. PMID:25004106

  19. Signatures of host/symbiont genome coevolution in insect nutritional endosymbioses

    PubMed Central

    Wilson, Alex C. C.; Duncan, Rebecca P.

    2015-01-01

    The role of symbiosis in bacterial symbiont genome evolution is well understood, yet the ways that symbiosis shapes host genomes or more particularly, host/symbiont genome coevolution in the holobiont is only now being revealed. Here, we identify three coevolutionary signatures that characterize holobiont genomes. The first signature, host/symbiont collaboration, arises when completion of essential pathways requires host/endosymbiont genome complementarity. Metabolic collaboration has evolved numerous times in the pathways of amino acid and vitamin biosynthesis. Here, we highlight collaboration in branched-chain amino acid and pantothenate (vitamin B5) biosynthesis. The second coevolutionary signature is acquisition, referring to the observation that holobiont genomes acquire novel genetic material through various means, including gene duplication, lateral gene transfer from bacteria that are not their current obligate symbionts, and full or partial endosymbiont replacement. The third signature, constraint, introduces the idea that holobiont genome evolution is constrained by the processes governing symbiont genome evolution. In addition, we propose that collaboration is constrained by the expression profile of the cell lineage from which endosymbiont-containing host cells, called bacteriocytes, are derived. In particular, we propose that such differences in bacteriocyte cell lineage may explain differences in patterns of host/endosymbiont metabolic collaboration between the sap-feeding suborders Sternorrhyncha and Auchenorrhynca. Finally, we review recent studies at the frontier of symbiosis research that are applying functional genomic approaches to characterization of the developmental and cellular mechanisms of host/endosymbiont integration, work that heralds a new era in symbiosis research. PMID:26039986

  20. Non-breeding habitat preference affects ecological speciation in migratory waders

    NASA Astrophysics Data System (ADS)

    Kraaijeveld, Ken

    2008-04-01

    Models of ecological speciation predict that certain types of habitat should be more conducive to species diversification than others. In this study, I test this hypothesis in waders of the sub-order Charadrii using the number of morphological sub-species per species as an index of diversity. I classified all members of this clade as spending the non-breeding season either coastally or inland and argue that these represent fundamentally different environments. Coastal mudflats are characterised by high predictability and patchy worldwide distribution, whilst inland wetlands are widespread but unpredictable. The results show that migratory species that winter coastally are sub-divided into more sub-species than those that winter inland. This was not the case for non-migratory species. I argue that coastal environments select for more rigid migratory pathways, whilst inland wetlands favour more flexible movement patterns. Population sub-division could then result from the passive segregation of breeding sites or from the active selection for assortative mating of ecomorphs.

  1. A divergent Cardinium found in daddy long-legs (Arachnida: Opiliones).

    PubMed

    Chang, Jin; Masters, Amber; Avery, Amanda; Werren, John H

    2010-11-01

    Recent studies indicate that a newly described bacterial endosymbiont, Cardinium, is widespread in arthropods and induces different reproductive manipulations in hosts. In this study, we used a portion of the 16S rRNA gene of the Cardinium to screen 16 Opilionid species from the suborder Palptores. We found the incidence of Cardinium in these Opiliones was significantly higher than in other pooled arthropods (31.2% versus 7.2%, P=0.007). Phylogenetic analyses using maximum parsimony (MP) and Bayesian analysis revealed two distinct clades in Opiliones. One is a divergent monophyletic clade with strong support that has so far not been found in other arthropods, and a second one contains Cardinium both from Opiliones and other arthropods. There is not complete concordance of the Cardinium strains with host phylogeny, suggesting some horizontal movement of the bacteria among Opiliones. Although the divergence in the sequenced 16S rRNA region between the Cardinium infecting Opiliones and Cardinium from other arthropods is greater than among Cardinium found in other arthropods, all are monophyletic with respect to the outgroup bacteria (endosymbionts of Acanthamoeba). Based on high pairwise genetic distances, deep branch, and a distinct phylogenetic grouping, we conclude that some Opiliones harbor a newly discovered Cardinium clade.

  2. Fauna Europaea – Orthopteroid orders

    PubMed Central

    Bohn, Horst; Haas, Fabian; Willemse, Fer

    2016-01-01

    Abstract Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all extant European terrestrial and freshwater animals, their geographical distribution at the level of countries and major islands (west of the Urals and excluding the Caucasus region), and some additional information. The Fauna Europaea project comprises about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. Fauna Europaea represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. The “Orthopteroid orders“ is one of the 58 Fauna Europaea major taxonomic groups. It contains series of mostly well-known insect orders: Embiodea (webspinners), Dermaptera (earwigs), Phasmatodea (walking sticks), Orthoptera s.s. (grasshoppers, crickets, bush-crickets) and Dictyoptera with the suborders Mantodea (mantids), Blattaria (cockroaches) and Isoptera (termites). For the Orthopteroid orders, data from 35 families containing 1,371 species are included in this paper. PMID:27660531

  3. Modulation of thermal noise and spectral sensitivity in Lake Baikal cottoid fish rhodopsins

    PubMed Central

    Luk, Hoi Ling; Bhattacharyya, Nihar; Montisci, Fabio; Morrow, James M.; Melaccio, Federico; Wada, Akimori; Sheves, Mudi; Fanelli, Francesca; Chang, Belinda S. W.; Olivucci, Massimo

    2016-01-01

    Lake Baikal is the deepest and one of the most ancient lakes in the world. Its unique ecology has resulted in the colonization of a diversity of depth habitats by a unique fauna that includes a group of teleost fish of the sub-order Cottoidei. This relatively recent radiation of cottoid fishes shows a gradual blue-shift in the wavelength of the absorption maximum of their visual pigments with increasing habitat depth. Here we combine homology modeling and quantum chemical calculations with experimental in vitro measurements of rhodopsins to investigate dim-light adaptation. The calculations, which were able to reproduce the trend of observed absorption maxima in both A1 and A2 rhodopsins, reveal a Barlow-type relationship between the absorption maxima and the thermal isomerization rate suggesting a link between the observed blue-shift and a thermal noise decrease. A Nakanishi point-charge analysis of the electrostatic effects of non-conserved and conserved amino acid residues surrounding the rhodopsin chromophore identified both close and distant sites affecting simultaneously spectral tuning and visual sensitivity. We propose that natural variation at these sites modulate both the thermal noise and spectral shifting in Baikal cottoid visual pigments resulting in adaptations that enable vision in deep water light environments. PMID:27934935

  4. Host specificity in Metamera sillasenorum, n. sp., a gregarine parasite of the leech Helobdella triserialis with notes on transmission dynamics.

    PubMed

    Wise, M R; Janovy, J; Wise, J C

    2000-06-01

    Eugregarines of the suborder Septatorina are apicomplexan parasites that are found mainly in arthropods. Some exceptions are species in the Metameridae that contains the only 5 septate gregarines recorded from annelids. The type genus is Metamera Duke, 1910 with 2 species, Metamera schubergi Duke, 1910, in European Glossiphonia complanata, and Metamera reynoldsi Jones, 1943, from North American G. complanata. Over the summers of 1995-1998, in Keith County, Nebraska, septate gregarines were found in the glossiphoniid leech Helobdella triserialis. The gregarines were determined to be a new species of Metamera, herein named Metamera sillasenorum. Measurements of size and body proportions of over 600 gregarines and 50 oocysts showed differences from measurements of M. schubergi and M. reynoldsi, and secondary septa in the deutomerite were rarely observed. Field observations indicated that M. sillasenorum is probably host specific. In the laboratory, leeches also exhibited strong feeding preferences; e.g., H. triserialis and G. complanata consumed only snails, whereas Helobdella stagnalis consumed only oligochaetes. Infection experiments demonstrated that freshwater snails ingest the oocysts and are required as mechanical vectors. Oocysts were passed unaltered through the snails' intestines. Glossiphonia complanata did not become infected regardless of heavy exposure to oocysts, although only 5 G. complanata were used in the experiments. The results show that host specificity of M. sillasenorum is most likely due to a combination of host-feeding habits and host-parasite compatibility.

  5. Purification, characterization and homology analysis of ocellatin 4, a cytolytic peptide from the skin secretion of the frog Leptodactylus ocellatus.

    PubMed

    Nascimento, Anna; Chapeaurouge, Alex; Perales, Jonas; Sebben, Antonio; Sousa, Marcelo V; Fontes, Wagner; Castro, Mariana S

    2007-12-15

    Neobatrachia is the amphibian suborder with the largest number of species and a most important source of bioactive peptides from frog skin secretions. However, 90% of the studies on this subject have been focused on the frog families Hylidae and Ranidae, while very little is known about peptides of other families, like Leptodactylidae. Our work reports for the first time the isolation and characterization of ocellatin 4 (GLLDFVTGVGKDIFAQLIKQI-NH(2)), a cytolytic peptide from the skin secretion of the South American frog Leptodactylus ocellatus. While most cytolytic amphibian skin peptides are selective for microorganisms and harmless for mammalian cells, the HC(50) of ocellatin 4 against human erythrocytes is 14.3muM. The interaction between ocellatin 4 and zwitterionic phospholipids in mammalian plasma membranes may be favored by its neutral charge at pH 7.0. Ocellatin 4 also shows some antibacterial activity (MICs(E. coli)(and)(S. aureus)=64muM) and its sequence shares similarities with the only six leptodactylid peptides previously known and with four peptides from Australian hylid frogs of the genus Litoria.

  6. Molecular phylogeny of Orthetrum dragonflies reveals cryptic species of Orthetrum pruinosum.

    PubMed

    Yong, Hoi Sen; Lim, Phaik-Eem; Tan, Ji; Ng, Yong Foo; Eamsobhana, Praphathip; Suana, I Wayan

    2014-07-03

    Dragonflies of the genus Orthetrum are members of the suborder Anisoptera, family Libellulidae. There are species pairs whose members are not easily separated from each other by morphological characters. In the present study, the DNA nucleotide sequences of mitochondrial and nuclear genes were employed to elucidate the phylogeny and systematics of Orthetrum dragonflies. Phylogenetic analyses could not resolve the various subfamilies of the family Libellulidae unequivocally. The nuclear 28S rRNA gene is highly conserved and could not resolve congeneric species of Orthetrum. Individual mitochondrial genes (COI, COII, and 16S rRNA) and combination of these genes as well as the nuclear ITS1&2 genes clearly differentiate morphologically similar species, such as the reddish species pairs O. chrysis and O. testaceum, and the bluish-coloured species O. glaucum and O. luzonicum. This study also reveals distinct genetic lineages between O. pruinosum schneideri (occurring in Malaysia) and O. pruinosum neglectum (occurring north of Peninsular Malaysia from India to Japan), indicating these taxa are cryptic species.

  7. Prey size selection and distance estimation in foraging adult dragonflies.

    PubMed

    Olberg, R M; Worthington, A H; Fox, J L; Bessette, C E; Loosemore, M P

    2005-09-01

    To determine whether perching dragonflies visually assess the distance to potential prey items, we presented artificial prey, glass beads suspended from fine wires, to perching dragonflies in the field. We videotaped the responses of freely foraging dragonflies (Libellula luctuosa and Sympetrum vicinum-Odonata, suborder Anisoptera) to beads ranging from 0.5 mm to 8 mm in diameter, recording whether or not the dragonflies took off after the beads, and if so, at what distance. Our results indicated that dragonflies were highly selective for bead size. Furthermore, the smaller Sympetrum preferred beads of smaller size and the larger Libellula preferred larger beads. Each species rejected beads as large or larger than their heads, even when the beads subtended the same visual angles as the smaller, attractive beads. Since bead size cannot be determined without reference to distance, we conclude that dragonflies are able to estimate the distance to potential prey items. The range over which they estimate distance is about 1 m for the larger Libellula and 70 cm for the smaller Sympetrum. The mechanism of distance estimation is unknown, but it probably includes both stereopsis and the motion parallax produced by head movements.

  8. The Beaver’s Phylogenetic Lineage Illuminated by Retroposon Reads

    PubMed Central

    Doronina, Liliya; Matzke, Andreas; Churakov, Gennady; Stoll, Monika; Huge, Andreas; Schmitz, Jürgen

    2017-01-01

    Solving problematic phylogenetic relationships often requires high quality genome data. However, for many organisms such data are still not available. Among rodents, the phylogenetic position of the beaver has always attracted special interest. The arrangement of the beaver’s masseter (jaw-closer) muscle once suggested a strong affinity to some sciurid rodents (e.g., squirrels), placing them in the Sciuromorpha suborder. Modern molecular data, however, suggested a closer relationship of beaver to the representatives of the mouse-related clade, but significant data from virtually homoplasy-free markers (for example retroposon insertions) for the exact position of the beaver have not been available. We derived a gross genome assembly from deposited genomic Illumina paired-end reads and extracted thousands of potential phylogenetically informative retroposon markers using the new bioinformatics coordinate extractor fastCOEX, enabling us to evaluate different hypotheses for the phylogenetic position of the beaver. Comparative results provided significant support for a clear relationship between beavers (Castoridae) and kangaroo rat-related species (Geomyoidea) (p < 0.0015, six markers, no conflicting data) within a significantly supported mouse-related clade (including Myodonta, Anomaluromorpha, and Castorimorpha) (p < 0.0015, six markers, no conflicting data). PMID:28256552

  9. How Does Environmental Variation Affect the Distribution of Dragonfly Larvae (Odonata) in the Amazon-Cerrado Transition Zone in Central Brazil?

    PubMed

    Mendes, T P; Luiza-Andrade, A; Cabette, H S R; Juen, L

    2017-03-11

    This study investigated the effects of environmental variation on assemblages of dragonfly larvae (Odonata). We hypothesize that there is a significant correlation between species richness, species composition, and abundance of Odonata individuals, and habitat integrity and abiotic variables. To test this hypothesis, we sampled odonate larvae at 12 streams in the Suiá-Miçú River basin in Mato Grosso, Brazil, during three different periods of the year. Local physical and chemical variables (temperature, pH, turbidity, electrical conductivity (EC), dissolved oxygen (DO), total dissolved solids (TDS), and oxidation reduction potential (ORP)) were measured at each site using a multi-parameter probe, and integrity was assessed using the Habitat Integrity Index (HII). The variation in richness, abundance, and composition of Odonata species was related to the environmental variables analyzed, primarily by the abiotic factors pH, electrical conductivity, dissolved oxygen, total dissolved solids, and oxidation reduction potential. Our hypothesis was corroborated for the suborder Anisoptera, which showed a significant relationship with these variables, whereas Zygoptera was only related to pH. Our results show the importance of physical and chemical conditions in ecological studies using Odonata larvae as tools for the management and conservation of freshwater ecosystems.

  10. Comparative Cytogenetics between Two Important Songbird, Models: The Zebra Finch and the Canary.

    PubMed

    Dos Santos, Michelly da Silva; Kretschmer, Rafael; Frankl-Vilches, Carolina; Bakker, Antje; Gahr, Manfred; O Brien, Patricia C M; Ferguson-Smith, Malcolm A; de Oliveira, Edivaldo H C

    2017-01-01

    Songbird species (order Passeriformes, suborder Oscines) are important models in various experimental fields spanning behavioural genomics to neurobiology. Although the genomes of some songbird species were sequenced recently, the chromosomal organization of these species is mostly unknown. Here we focused on the two most studied songbird species in neuroscience, the zebra finch (Taeniopygia guttata) and the canary (Serinus canaria). In order to clarify these issues and also to integrate chromosome data with their assembled genomes, we used classical and molecular cytogenetics in both zebra finch and canary to define their chromosomal homology, localization of heterochromatic blocks and distribution of rDNA clusters. We confirmed the same diploid number (2n = 80) in both species, as previously reported. FISH experiments confirmed the occurrence of multiple paracentric and pericentric inversions previously found in other species of Passeriformes, providing a cytogenetic signature for this order, and corroborating data from in silico analyses. Additionally, compared to other Passeriformes, we detected differences in the zebra finch karyotype concerning the morphology of some chromosomes, in the distribution of 5S rDNA clusters, and an inversion in chromosome 1.

  11. Hystricognathy vs Sciurognathy in the Rodent Jaw: A New Morphometric Assessment of Hystricognathy Applied to the Living Fossil Laonastes (Diatomyidae)

    PubMed Central

    Hautier, Lionel; Lebrun, Renaud; Saksiri, Soonchan; Michaux, Jacques; Vianey-Liaud, Monique; Marivaux, Laurent

    2011-01-01

    While exceptional for an intense diversification of lineages, the evolutionary history of the order Rodentia comprises only a limited number of morphological morphotypes for the mandible. This situation could partly explain the intense debates about the taxonomic position of the latest described member of this clade, the Laotian rock rat Laonastes aenigmamus (Diatomyidae). This discovery has re-launched the debate on the definition of the Hystricognathi suborder identified using the angle of the jaw relative to the plane of the incisors. Our study aims to end this ambiguity. For clarity, it became necessary to revisit the entire morphological diversity of the mandible in extant and extinct rodents. However, current and past rodent diversity brings out the limitations of the qualitative descriptive approach and highlights the need for a quantitative approach. Here, we present the first descriptive comparison of the masticatory apparatus within the Ctenohystrica clade, in combining classic comparative anatomy with morphometrical methods. First, we quantified the shape of the mandible in rodents using 3D landmarks. Then, the analysis of osteological features was compared to myological features in order to understand the biomechanical origin of this morphological diversity. Among the morphological variation observed, the mandible of Laonastes aenigmamus displays an intermediate association of features that could be considered neither as sciurognathous nor as hystricognathous. PMID:21490933

  12. Sperm Cells of a Primitive Strepsipteran

    PubMed Central

    Nardi, James B.; Delgado, Juan A.; Collantes, Francisco; Miller, Lou Ann; Bee, Charles M.; Kathirithamby, Jeyaraney

    2013-01-01

    The unusual life style of Strepsiptera has presented a long-standing puzzle in establishing its affinity to other insects. Although Strepsiptera share few structural similarities with other insect orders, all members of this order share a parasitic life style with members of two distinctive families in the Coleoptera—the order now considered the most closely related to Strepsiptera based on recent genomic evidence. Among the structural features of several strepsipteran families and other insect families that have been surveyed are the organization of testes and ultrastructure of sperm cells. For comparison with existing information on insect sperm structure, this manuscript presents a description of testes and sperm of a representative of the most primitive extant strepsipteran family Mengenillidae, Eoxenos laboulbenei. We compare sperm structure of E. laboulbenei from this family with that of the three other families of Strepsiptera in the other strepsipteran suborder Stylopidia that have been studied as well as with members of the beetle families Meloidae and Rhipiphoridae that share similar life histories with Strepsiptera. Meloids, Rhipiphorids and Strepsipterans all begin larval life as active and viviparous first instar larvae. This study examines global features of these insects’ sperm cells along with specific ultrastructural features of their organelles. PMID:26462430

  13. Sperm Cells of a Primitive Strepsipteran.

    PubMed

    Nardi, James B; Delgado, Juan A; Collantes, Francisco; Miller, Lou Ann; Bee, Charles M; Kathirithamby, Jeyaraney

    2013-09-04

    The unusual life style of Strepsiptera has presented a long-standing puzzle in establishing its affinity to other insects. Although Strepsiptera share few structural similarities with other insect orders, all members of this order share a parasitic life style with members of two distinctive families in the Coleoptera-the order now considered the most closely related to Strepsiptera based on recent genomic evidence. Among the structural features of several strepsipteran families and other insect families that have been surveyed are the organization of testes and ultrastructure of sperm cells. For comparison with existing information on insect sperm structure, this manuscript presents a description of testes and sperm of a representative of the most primitive extant strepsipteran family Mengenillidae, Eoxenos laboulbenei. We compare sperm structure of E. laboulbenei from this family with that of the three other families of Strepsiptera in the other strepsipteran suborder Stylopidia that have been studied as well as with members of the beetle families Meloidae and Rhipiphoridae that share similar life histories with Strepsiptera. Meloids, Rhipiphorids and Strepsipterans all begin larval life as active and viviparous first instar larvae. This study examines global features of these insects' sperm cells along with specific ultrastructural features of their organelles.

  14. Analog number representations in mongoose lemurs (Eulemur mongoz): evidence from a search task.

    PubMed

    Lewis, Kerrie P; Jaffe, Sarah; Brannon, Elizabeth M

    2005-10-01

    A wealth of data demonstrating that monkeys and apes represent number have been interpreted as suggesting that sensitivity to number emerged early in primate evolution, if not before. Here we examine the numerical capacities of the mongoose lemur (Eulemur mongoz), a member of the prosimian suborder of primates that split from the common ancestor of monkeys, apes and humans approximately 47-54 million years ago. Subjects observed as an experimenter sequentially placed grapes into an opaque bucket. On half of the trials the experimenter placed a subset of the grapes into a false bottom such that they were inaccessible to the lemur. The critical question was whether lemurs would spend more time searching the bucket when food should have remained in the bucket, compared to when they had retrieved all of the food. We found that the amount of time lemurs spent searching was indicative of whether grapes should have remained in the bucket, and furthermore that lemur search time reliably differentiated numerosities that differed by a 1:2 ratio, but not those that differed by a 2:3 or 3:4 ratio. Finally, two control conditions determined that lemurs represented the number of food items, and neither the odor of the grapes, nor the amount of grape (e.g., area) in the bucket. These results suggest that mongoose lemurs have numerical representations that are modulated by Weber's Law.

  15. Modulation of thermal noise and spectral sensitivity in Lake Baikal cottoid fish rhodopsins.

    PubMed

    Luk, Hoi Ling; Bhattacharyya, Nihar; Montisci, Fabio; Morrow, James M; Melaccio, Federico; Wada, Akimori; Sheves, Mudi; Fanelli, Francesca; Chang, Belinda S W; Olivucci, Massimo

    2016-12-09

    Lake Baikal is the deepest and one of the most ancient lakes in the world. Its unique ecology has resulted in the colonization of a diversity of depth habitats by a unique fauna that includes a group of teleost fish of the sub-order Cottoidei. This relatively recent radiation of cottoid fishes shows a gradual blue-shift in the wavelength of the absorption maximum of their visual pigments with increasing habitat depth. Here we combine homology modeling and quantum chemical calculations with experimental in vitro measurements of rhodopsins to investigate dim-light adaptation. The calculations, which were able to reproduce the trend of observed absorption maxima in both A1 and A2 rhodopsins, reveal a Barlow-type relationship between the absorption maxima and the thermal isomerization rate suggesting a link between the observed blue-shift and a thermal noise decrease. A Nakanishi point-charge analysis of the electrostatic effects of non-conserved and conserved amino acid residues surrounding the rhodopsin chromophore identified both close and distant sites affecting simultaneously spectral tuning and visual sensitivity. We propose that natural variation at these sites modulate both the thermal noise and spectral shifting in Baikal cottoid visual pigments resulting in adaptations that enable vision in deep water light environments.

  16. [Peculiarities of ultrastructure of excretory system in Bothrioplana semperi (Platyhelminthes, Turbellaria)].

    PubMed

    Kornakova, E E

    2010-01-01

    Ultrastructural study of morphology of cirtocytes and excretory channels was performed in the free living turbellaria Bothrioplana semperi (Turbellaria, Seriata). It has been shown that cirtocytes of this species are formed by two cells--the terminal and the proximal cells of the channel. The fan is composed of two rod rows. The external row goes out from the terminal cell, the internal one is a derivate of the channel proximal cell. Inside each rod of the external row there runs a bundle of microfilaments; it originates in the cytoplasm of the channel proximal cell distal to bases of the external rods. On the internal rod membranes there are noted small electrondense granules disposed separately or fused in the solid layer continuing into a dense "membrane" connecting rods of the external and internal rows. Rare internal leptotrichiae go out from the cirtocyte cavity bottom. External leptotrichiae are absent. The septate desmosome at the level of the terminal cell is absent, but is present in the channel proximal cell at the level of terminal of cilia. The apical surface of the channel cell carries rare short microvilli. The basement membrane of cells of excretory channels forms deep invaginations almost reaching the apical membrane. Epithelium of excretory channels is deprived of cilia. Ultrastructure of cirtocytes and excretory channels of B. semperi is similar to those in representatives of the suborder Proseriata (Seriata). The significance of ultrastructure of the Proseriata cirtocytes, especially of the order of formation of versh, for construction of phylogeny of Platyhelminthes is discussed.

  17. Phylogeny of Dictyoptera: Dating the Origin of Cockroaches, Praying Mantises and Termites with Molecular Data and Controlled Fossil Evidence.

    PubMed

    Legendre, Frédéric; Nel, André; Svenson, Gavin J; Robillard, Tony; Pellens, Roseli; Grandcolas, Philippe

    2015-01-01

    Understanding the origin and diversification of organisms requires a good phylogenetic estimate of their age and diversification rates. This estimate can be difficult to obtain when samples are limited and fossil records are disputed, as in Dictyoptera. To choose among competing hypotheses of origin for dictyopteran suborders, we root a phylogenetic analysis (~800 taxa, 10 kbp) within a large selection of outgroups and calibrate datings with fossils attributed to lineages with clear synapomorphies. We find the following topology: (mantises, (other cockroaches, (Cryptocercidae, termites)). Our datings suggest that crown-Dictyoptera-and stem-mantises-would date back to the Late Carboniferous (~ 300 Mya), a result compatible with the oldest putative fossil of stem-dictyoptera. Crown-mantises, however, would be much more recent (~ 200 Mya; Triassic/Jurassic boundary). This pattern (i.e., old origin and more recent diversification) suggests a scenario of replacement in carnivory among polyneopterous insects. The most recent common ancestor of (cockroaches + termites) would date back to the Permian (~275 Mya), which contradicts the hypothesis of a Devonian origin of cockroaches. Stem-termites would date back to the Triassic/Jurassic boundary, which refutes a Triassic origin. We suggest directions in extant and extinct species sampling to sharpen this chronological framework and dictyopteran evolutionary studies.

  18. Data for comparative proteomics of ovaries from five non-model, crustacean amphipods☆

    PubMed Central

    Trapp, Judith; Almunia, Christine; Gaillard, Jean-Charles; Pible, Olivier; Chaumot, Arnaud; Geffard, Olivier; Armengaud, Jean

    2015-01-01

    Ovaries were taken from five sexually mature amphipods: Gammarus fossarum, Gammarus pulex, Gammarus roeseli, Hyallela azteca and Parhyale hawaiensis. The soluble proteome extracted from individual pair of ovaries from five biological replicates was trypsin digested and the resulting peptides were analyzed by high resolution tandem mass spectrometry. The spectra were assigned with four protein sequence databases with different specificities: a RNAseq-derived G. fossarum database; a RNAseq-derived P. hawaiensis database; both originating from ovaries transcriptome; the Daphnia pulex database derived from whole-genome sequencing and the NCBInr database. The best interpretation was obtained for most animals with the specific RNA-seq protein database previously established by means of RNAseq carried out on G. fossarum. Proteins identified in the five amphipod species allow defining the core-proteome of female reproductive tissues of the Senticaudata suborder. The data accompanying the manuscript describing the database searches and comparative analysis Trapp et al., 2015 [1] have been deposited to the ProteomeXchange with identifiers PXD002253 (G. fossarum), PXD002254 (G. pulex), PXD002255 (G. roeseli), PXD002256 (H. Azteca), and PXD002257 (P. hawaiensis). PMID:26380837

  19. Comparison of intraspecific, interspecific and intergeneric chloroplast diversity in Cycads.

    PubMed

    Jiang, Guo-Feng; Hinsinger, Damien Daniel; Strijk, Joeri Sergej

    2016-08-25

    Cycads are among the most threatened plant species. Increasing the availability of genomic information by adding whole chloroplast data is a fundamental step in supporting phylogenetic studies and conservation efforts. Here, we assemble a dataset encompassing three taxonomic levels in cycads, including ten genera, three species in the genus Cycas and two individuals of C. debaoensis. Repeated sequences, SSRs and variations of the chloroplast were analyzed at the intraspecific, interspecific and intergeneric scale, and using our sequence data, we reconstruct a phylogenomic tree for cycads. The chloroplast was 162,094 bp in length, with 133 genes annotated, including 87 protein-coding, 37 tRNA and 8 rRNA genes. We found 7 repeated sequences and 39 SSRs. Seven loci showed promising levels of variations for application in DNA-barcoding. The chloroplast phylogeny confirmed the division of Cycadales in two suborders, each of them being monophyletic, revealing a contradiction with the current family circumscription and its evolution. Finally, 10 intraspecific SNPs were found. Our results showed that despite the extremely restricted distribution range of C. debaoensis, using complete chloroplast data is useful not only in intraspecific studies, but also to improve our understanding of cycad evolution and in defining conservation strategies for this emblematic group.

  20. A phylogeny of cycads (Cycadales) inferred from chloroplast matK gene, trnK intron, and nuclear rDNA ITS region.

    PubMed

    Chaw, Shu-Miaw; Walters, Terrence W; Chang, Chien-Chang; Hu, Shu-Hsuan; Chen, Shin-Hsiao

    2005-10-01

    Phylogenetic relationships among the three families and 12 living genera of cycads were reconstructed by distance and parsimony criteria using three markers: the chloroplast matK gene, the chloroplast trnK intron and the nuclear ITS/5.8S rDNA sequence. All datasets indicate that Cycadaceae (including only the genus Cycas) is remotely related to other cycads, in which Dioon was resolved as the basal-most clade, followed by Bowenia and a clade containing the remaining nine genera. Encephalartos and Lepidozamia are closer to each other than to Macrozamia. The African genus Stangeria is embedded within the New World subfamily Zamiodeae. Therefore, Bowenia is an unlikely sister to Stangeria, contrary to the view that they form the Stangeriaceae. The generic status of Dyerocycas and Chigua is unsupportable as they are paraphyletic with Cycas and the Zamia, respectively. Nonsense mutations in the matK gene and indels in the other two datasets lend evidence to reinforce the above conclusions. According to the phylogenies, the past geography of the genera of cycads and the evolution of character states are hypothesized and discussed. Within the suborder Zamiieae, Stangeria, and the tribe Zamieae evolved significantly faster than other genera. The matK gene and ITS/5.8S region contain more useful information than the trnK intron in addressing phylogeny. Redelimitations of Zamiaceae, Stangeriaceae, subfamily Encephalartoideae and subtribe Macrozamiineae are necessary.

  1. Mitochondrial genomic investigation of flatfish monophyly.

    PubMed

    Campbell, Matthew A; López, J Andrés; Satoh, Takashi P; Chen, Wei-Jen; Miya, Masaki

    2014-11-10

    We present the first study to use whole mitochondrial genome sequences to examine phylogenetic affinities of the flatfishes (Pleuronectiformes). Flatfishes have attracted attention in evolutionary biology since the early history of the field because understanding the evolutionary history and patterns of diversification of the group will shed light on the evolution of novel body plans. Because recent molecular studies based primarily on DNA sequences from nuclear loci have yielded conflicting results, it is important to examine phylogenetic signal in different genomes and genome regions. We aligned and analyzed mitochondrial genome sequences from thirty-nine pleuronectiforms including nine that are newly reported here, and sixty-six non-pleuronectiforms (twenty additional clade L taxa [Carangimorpha or Carangimorpharia] and forty-six secondary outgroup taxa). The analyses yield strong support for clade L and weak support for the monophyly of Pleuronectiformes. The suborder Pleuronectoidei receives moderate support, and as with other molecular studies the putatively basal lineage of Pleuronectiformes, the Psettodoidei is frequently not most closely related to other pleuronectiforms. Within the Pleuronectoidei, the basal lineages in the group are poorly resolved, however several flatfish subclades receive consistent support. The affinities of Lepidoblepharon and Citharoides among pleuronectoids are particularly uncertain with these data.

  2. A multiple data set phylogeny for the endemic South African freshwater phreatoicidean isopod genus Mesamphisopus: Taxonomic and biogeographic implications.

    PubMed

    Gouws, G; Matthee, C A; Stewart, B A

    2010-05-01

    The obligate, freshwater isopod suborder Phreatoicidea is represented in South Africa by ten species contained within the endemic genus Mesamphisopus (Mesamphisopidae). Here, phylogenetic hypotheses are proposed to describe the evolutionary and biogeographic history of the genus with respect to drainage basin evolution and to assess species diversity, particularly among populations variably identified as Mesamphisopusabbreviatus or Mesamphisopusdepressus. Twenty-three ingroup taxa were examined, including eight known species and representatives of the M. abbreviatus-depressus complex. Allozyme data from 12 loci were analysed phenetically and cladistically. Mitochondrial DNA sequence data from the 12S ribosomal RNA and cytochrome c oxidase subunit I genes were analysed as a combined mtDNA data set and as a total data set in combination with recoded allele frequency data. Analyses retrieved (1) a monophyletic Mesamphisopus; (2) Mesamphisopustsitsikamma and a Mesamphisopuspaludosus+Mesamphisopuspenicillatus clade as basal lineages; (3) a Mesamphisopuscapensis+Mesamphisopusbaccatus clade; and (4) a clade containing the M. abbreviatus-depressus complex, with these taxa nested among several other species. Large genetic distances among taxa and the paraphyly of the members of the M. abbreviatus-depressus complex suggested the presence of hidden taxonomic diversity in Mesamphisopus. Clear biogeographic patterns emerged with lineages and clades mostly restricted to geographically discrete regions. Patterns showed remarkable similarity to those seen in the region's terrestrial fauna and bore no relation to the history of drainage basins. These patterns suggested that vicariance and, possibly, limited dispersal events played a major role in the evolution of Mesamphisopus.

  3. All Rodents Are Not the Same: A Modern Synthesis of Cortical Organization

    PubMed Central

    Krubitzer, Leah; Campi, Katharine L.; Cooke, Dylan F.

    2011-01-01

    Rodents are a major order of mammals that is highly diverse in distribution and lifestyle. Five suborders, 34 families, and 2,277 species within this order occupy a number of different niches and vary along several lifestyle dimensions such as diel pattern (diurnal vs. nocturnal), terrain niche, and diet. For example, the terrain niche of rodents includes arboreal, aerial, terrestrial, semi-aquatic, burrowing, and rock dwelling. Not surprisingly, the behaviors associated with particular lifestyles are also highly variable and thus the neocortex, which generates these behaviors, has undergone corresponding alterations across species. Studies of cortical organization in species that vary along several dimensions such as terrain niche, diel pattern, and rearing conditions demonstrate that the size and number of cortical fields can be highly variable within this order. The internal organization of a cortical field also reflects lifestyle differences between species and exaggerates behaviorally relevant effectors such as vibrissae, teeth, or lips. Finally, at a cellular level, neuronal number and density varies for the same cortical field in different species and is even different for the same species reared in different conditions (laboratory vs. wild-caught). These very large differences across and within rodent species indicate that there is no generic rodent model. Rather, there are rodent models suited for specific questions regarding the development, function, and evolution of the neocortex. PMID:21701141

  4. Molecular evidence for multiple origins of Insectivora and for a new order of endemic African insectivore mammals.