The complete genome sequence and phylogenetic analysis of the mitochondrial DNA of the wood-decaying fungus <Emphasis Type="Italic">Fomitopsis palustris</Emphasis>

The complete mitochondrial genome sequence of the wood-decaying fungus Fomitopsis palustris (Basidiomycete, Agaricomycotina) was determined by next-generation sequencing technology. The complete sequence of the circular mitochondrial DNA of F. palustris was 63,479 bp in length with a 75.98% AT content. The mitochondrial genome encoded 14 conserved proteins, 2 ribosomal RNAs, 26 transfer RNAs, and 19 additional open reading frames. The coxI and cob genes contained six and one group I introns, respectively, and encoded eight open reading frames, including seven intron-encoded endonucleases. The complete mitochondrial genome of F. palustris presented herein represents the first such report for brown rot basidiomycetes. In addition, the BLAST score ratio and phylogenetic analysis may open new avenues to understanding the evolutionary status of this fungus .     

Cytochrome oxidase deficiency during development of amphibian nucleocytoplasmic hybrids.

The activity of mitochondrial cytochrome oxidase was investigated during the embryonic development of nucleocytoplasmic hybrids containing a nuclear genome derived from R. pipiens and a mitochondrial genome derived from R. palustris. Using a quantitative cytochemical approach, we found that the activity of cytochrome oxidase failed to increase during the development of these embryos. Control embryos containing a haploid chromosomal complement, derived from the same species as that from which the maternally inherited mitochondria is derived and hybrid crosses between R. palustris and R. pipiens, showed a significant increase in cytochrome oxidase activity during development. Oxygen uptake data from diploid and haploid R. pipiens embryos were in agreement with the data obtained by the cytochemical method. These results indicate that a normal pattern of cytochrome oxidase activity during embryonic development requires a nuclear genome which contains a haploid chromosomal complement derived from the same species as that from which the mitochondrial genome is derived.     

Tylenchulus palustris Parasitizing Peach Trees in the of nited States

Most morphological characteristics of three populations of a Tylenchulus sp. from peach roots in Alabama, Arkansas, and Georgia did not differ from those of T. palustris paratypes. However, some mature females differed slightly from those of T. palustris paratypes from Florida. These mature females were more swollen in the posterior portion of their bodies, and they possessed digitate postvulval body sections with round rather than conoid termini. These morphological variants had a wide postvulval section core (PVSC), as do T. palustris paratypes; they did not differ from the paratypes in other characteristics. Second-stage juveniles and males were less morphologically variable and were not different from the paratypes. No males were found in populations from Alabama and Georgia. The Tylenchulus sp. from three peach sites was determined to be T. palustris. This is the first report of T. palustris on an economically important crop.     

Cytogeographical survey ofEleocharis subser.Eleocharis in Europe 1:Eleocharis palustris

Chromosome numbers forEleocharis palustris subsp.palustris (based on 70 samples from Austria, Bulgaria, Croatia, the Czech Republic, Germany, Greece, Hungary, Lithuania, Romania, Russia, Slovakia, Slovenia, and Sweden) andEleocharis palustris subsp.vulgaris (based on 74 samples from Austria, the Czech Republic, Denmark, Germany, Ireland, Latvia, Luxembourg, the Netherlands, Portugal, and Sweden) are given. Also the chromosome number estimates based on relative DNA contents of plants from 8 localitiesE. palustris subsp.palustris from Croatia, the Czech Republic, Germany, Italy, Israel, and Slovenia, and from 18 localities ofE. palustris subsp.vulgaris from the Czech Republic, Germany and Sweden are included. InE. palustris subsp.palustris, 2n=16 prevailed, the mixoploid 2n=15, 16 was rare and a lone hypoploid 2n=15 was detected. InE. palustris subsp.vulgaris 2n=38 was most frequently detected, the hyperploid 2n=39 and mixoploid 2n=38, 39 were common, and the hypoploid 2n=36 and mixoploids in which 2n ranges from 36 to 42 were rarer. Distribution maps based on plants investigated either by chromosome counting or by flow cytometry, augmented by similar data from published sources are given for both subspecies in Europe.     

Feeding preferences and food searching strategies mediated by air- and water-borne cues in the mud whelk Terebralia palustris (Potamididae: Gastropoda)

The gastropod T. palustris is one of the major species responsible for leaf consumption and degration within the Indo-Pacific mangrove forests, and it strongly competes with herbivorous sesarmid crabs in consuming fallen leaves. This snail feeds at high and low tides and it is able to locate food items by means of chemical cues. The aim of this study was to assess the food preferences of T. palustris and to define its feeding strategies at low and high tides, by conducting field trials on water-borne mediated food location at high tide, grazing rate and the chemical attraction exerted by different mangrove leaves. The results showed that T. palustris was able to perceive underwater grazed leaves. In addition, we demonstrated that T. palustris consumes all the mangrove species (preferentially the Rhizophoraceae leaves) but Xilocarpus granatum. Moreover, this snail is differentially attracted to different mangrove species: the major attractive power is wielded by the rhizophoracean species and Pemphis acidula, while X. granatum does not attract this snail at all. The efficacy and adaptive value of a chemically mediated food searching strategies is unquestionable since by using this ability T. palustris can locate and reach the leaves it preferentially consumes. Moreover, T. palustris is the only macrobenthic species of East Africa mangroves able to search, detect and consume mangrove leaves at both high and low tides. Such an expanded feeding window permits T. palustris to occupy temporal niches left empty by the sesarmid crabs.     

Evolution of low-light adapted peripheral light-harvesting complexes in strains of Rhodopseudomonas palustris

Purple bacteria have peripheral light-harvesting (PLH) complexes adapted to high-light (LH2) and low-light (LH3, LH4) growth conditions. The latter two have only been fully characterised in Rhodopseudomonas acidophila 7050 and Rhodopseudomonas palustris CGA009, respectively. It is known that LH4 complexes are expressed under the control of two light sensing bacteriophytochromes (BphPs). Recent genomic sequencing of a number of Rps. palustris strains has provided extensive information on PLH genes. We show that both LH3 and LH4 complexes are present in Rps. palustris and have evolved in the same operon controlled by the two adjacent BphPs. Two rare marker genes indicate that a gene cluster CL2, containing LH2 genes and the BphP RpBphP4, was internally transferred within the genome to form a new operon CL1. In CL1, RpBphP4 underwent gene duplication to RpBphP2 and RpBphP3, which evolved to sense light intensity rather than spectral red/far-red intensity ratio. We show that a second LH2 complex was acquired in CL1 belonging to a different PLH clade and these two PLH complexes co-evolved together into LH3 or LH4 complexes. The near-infrared spectra provide additional support for our conclusions on the evolution of PLH complexes based on genomic data.     

Sequence Analysis of the Cryptic Plasmid pMG101 from Rhodopseudomonas palustris and Construction of Stable Cloning Vectors

A 15-kb cryptic plasmid was obtained from a natural isolate of Rhodopseudomonas palustris. The plasmid, designated pMG101, was able to replicate in R. palustris and in closely related strains of Bradyrhizobium japonicum and phototrophic Bradyrhizobium species. However, it was unable to replicate in the purple nonsulfur bacterium Rhodobacter sphaeroides and in Rhizobium species. The replication region of pMG101 was localized to a 3.0-kb SalI-XhoI fragment, and this fragment was stably maintained in R. palustris for over 100 generations in the absence of selection. The complete nucleotide sequence of this fragment revealed two open reading frames (ORFs), ORF1 and ORF2. The deduced amino acid sequence of ORF1 is similar to sequences of Par proteins, which mediate plasmid stability from certain plasmids, while ORF2 was identified as a putative rep gene, coding for an initiator of plasmid replication, based on homology with the Rep proteins of several other plasmids. The function of these sequences was studied by deletion mapping and gene disruptions of ORF1 and ORF2. pMG101-based Escherichia coli-R. palustris shuttle cloning vectors pMG103 and pMG105 were constructed and were stably maintained in R. palustris growing under nonselective conditions. The ability of plasmid pMG101 to replicate in R. palustris and its close phylogenetic relatives should enable broad application of these vectors within this group of α-proteobacteria.     

Comparative study on the essential oils of Myosotis arvensis and Myosotis palustris herbs (Boraginaceae)

The essential oils were obtained from Myosotis arvensis L. and M. palustris L. by hydrodistillation and subsequently analyzed by GC–MS. Fifteen components in M. arvensis and twenty-one in M. palustris representing, respectively, 89.63 and 93.19 % of the total oils were identified on the basis of their retention time, mass spectra characteristics and semi-quantitative data were obtained from relative peak area percentages. The 3-methyl-benzaldehyde was found to be the major constituent of both tested oils (42.76 % in M. arvensis and 45.80 % in M. palustris). Additionally, methyl salicylate was a characteristic compound for M. arvensis and α-bisabolol oxide B for M. palustris.     

Enhanced hydrogen production by Rhodopseudomonas palustris CQK 01 with ultra-sonication pretreatment in batch culture

In the present study, the photo-hydrogen production performances by Rhodopseudomonas palustris CQK 01 growing from the inoculated cells with ultra-sonication pretreatment (R. palustris CQK 01-USP) were experimentally investigated in batch culture and compared with that without pretreatment (R. palustris CQK 01-NP). It was found that the ultra-sonication pretreatment modified membrane morphology and broke up part of the cells, resulting in improvement of membrane permeability and bacterial activities and hence, helping the improvement of hydrogen production. The hydrogen production rate, hydrogen yield and energy conversion efficiency with R. palustris CQK 01-USP were increased to be nearly 2 times higher than that with R. palustris CQK 01-NP. The parametric study showed that under the conditions of initial glucose concentration 50 mmol/l, inoculum size 12%, illumination wavelength 590 nm, the photobioreactor with R. palustris CQK 01-USP obtained the optimal hydrogen production rate 0.54 mmol/l/h, hydrogen yield 1.2 mol-H₂/mol-glucose and energy conversion efficiency 9.03%.     

Experimental and Computational Investigation of Biofilm Formation by Rhodopseudomonas palustris Growth under Two Metabolic Modes

We examined biofilms formed by the metabolically versatile bacterium Rhodopseudomonas palustris grown via different metabolic modes. R. palustris was grown in flow cell chambers with identical medium conditions either in the presence or absence of light and oxygen. In the absence of oxygen and the presence of light, R. palustris grew and formed biofilms photoheterotrophically, and in the presence of oxygen and the absence of light, R. palustris grew and formed biofilms heterotrophically. We used confocal laser scanning microscopy and image analysis software to quantitatively analyze and compare R. palustris biofilm formation over time in these two metabolic modes. We describe quantifiable differences in structure between the biofilms formed by the bacterium grown heterotrophically and those grown photoheterotrophically. We developed a computational model to explore ways in which biotic and abiotic parameters could drive the observed biofilm architectures, as well as a random-forest machine-learning algorithm based on structural differences that was able to identify growth conditions from the confocal imaging of the biofilms with 87% accuracy. Insight into the structure of phototrophic biofilms and conditions that influence biofilm formation is relevant for understanding the generation of biofilm structures with different properties, and for optimizing applications with phototrophic bacteria growing in the biofilm state.     

Genome Sequence of the Chemolithoautotrophic Nitrite-Oxidizing Bacterium Nitrobacter winogradskyi Nb-255

The alphaproteobacterium Nitrobacter winogradskyi (ATCC 25391) is a gram-negative facultative chemolithoautotroph capable of extracting energy from the oxidation of nitrite to nitrate. Sequencing and analysis of its genome revealed a single circular chromosome of 3,402,093 bp encoding 3,143 predicted proteins. There were extensive similarities to genes in two alphaproteobacteria, Bradyrhizobium japonicum USDA110 (1,300 genes) and Rhodopseudomonas palustris CGA009 CG (815 genes). Genes encoding pathways for known modes of chemolithotrophic and chemoorganotrophic growth were identified. Genes encoding multiple enzymes involved in anapleurotic reactions centered on C₂ to C₄ metabolism, including a glyoxylate bypass, were annotated. The inability of N. winogradskyi to grow on C₆ molecules is consistent with the genome sequence, which lacks genes for complete Embden-Meyerhof and Entner-Doudoroff pathways, and active uptake of sugars. Two gene copies of the nitrite oxidoreductase, type I ribulose-1,5-bisphosphate carboxylase/oxygenase, cytochrome c oxidase, and gene homologs encoding an aerobic-type carbon monoxide dehydrogenase were present. Similarity of nitrite oxidoreductases to respiratory nitrate reductases was confirmed. Approximately 10% of the N. winogradskyi genome codes for genes involved in transport and secretion, including the presence of transporters for various organic-nitrogen molecules. The N. winogradskyi genome provides new insight into the phylogenetic identity and physiological capabilities of nitrite-oxidizing bacteria. The genome will serve as a model to study the cellular and molecular processes that control nitrite oxidation and its interaction with other nitrogen-cycling processes.     

Reductive, Coenzyme A-Mediated Pathway for 3-Chlorobenzoate Degradation in the Phototrophic Bacterium Rhodopseudomonas palustris

We isolated a strain of Rhodopseudomonas palustris (RCB100) by selective enrichment in light on 3-chlorobenzoate to investigate the steps that it uses to accomplish anaerobic dechlorination. Analyses of metabolite pools as well as enzyme assays suggest that R. palustris grows on 3-chlorobenzoate by (i) converting it to 3-chlorobenzoyl coenzyme A (3-chlorobenzoyl–CoA), (ii) reductively dehalogenating 3-chlorobenzoyl–CoA to benzoyl-CoA, and (iii) degrading benzoyl-CoA to acetyl-CoA and carbon dioxide. R. palustris uses 3-chlorobenzoate only as a carbon source and thus incorporates the acetyl-CoA that is produced into cell material. The reductive dechlorination route used by R. palustris for 3-chlorobenzoate degradation differs from those previously described in that a CoA thioester, rather than an unmodified aromatic acid, is the substrate for complete dehalogenation.     

Tylenchulus graminis n. sp. and T. palustris n. sp. (Tylenchulidae), from Native Flora of Florida,with Notes on T. semipenetrans and T. furcus

Tylenchulus graminis n. sp. and T. palustris n. sp. are described and illustrated from broomsedge (Andropogon virginicus L.) and pop ash (Fraxinus caroliniana Mill.), respectively. T. graminis resembles T. furcus in having a distinct anus, but T. graminis second-stage juveniles (J2) do not have a bifid tail. T. semipenetrans does not have a perceptible anus. The mature female of T. graminis has a mucronate pointed terminus while T. semipenetrans has a smooth and round terminus. T. graminis males have wider stylet knobs and basal bulb and a longer tail than T. semipenetrans males. T. graminis J2 have a longer posterior body portion (without large fat globules) than T. semipenetrans J2. T. palustris resembles T. semipenetrans in having an undetectable anus but differs by the short and conoid mature female postvulval section. The male of T. palustris has larger stylet knobs and basal bulb than those of T. semipenetrans and a bluntly rounded tail terminus, which is tapered in T. semipenetrans. T. palustris differs from T. furcus and T. graminis in having an undetectable anus, by the conoid postvulval section of mature females, by the shorter and rounded tail of males, and the shorter J2 posterior body section without large fat globules. T. graminis and T. palustris are parasites of indigenous flora of Florida.     

Genotypic and Phenotypic Diversity within Species of Purple Nonsulfur Bacteria Isolated from Aquatic Sediments

To assess the extent of genotypic and phenotypic diversity within species of purple nonsulfur bacteria found in aquatic sediments, a total of 128 strains were directly isolated from agar plates that had been inoculated with sediment samples from Haren and De Biesbosch in The Netherlands. All isolates were initially characterized by BOX-PCR genomic DNA fingerprinting, and 60 distinct genotypes were identified. Analyses of 16S rRNA gene sequences of representatives of each genotype showed that five and eight different phylotypes of purple nonsulfur bacteria were obtained from the Haren and De Biesbosch sites, respectively. At the Haren site, 80.5% of the clones were Rhodopseudomonas palustris, whereas Rhodoferax fermentans and Rhodopseudomonas palustris were numerically dominant at the De Biesbosch site and constituted 45.9 and 34.4% of the isolates obtained, respectively. BOX-PCR genomic fingerprints showed that there was a high level of genotypic diversity within each of these species. The genomic fingerprints of Rhodopseudomonas palustris isolates were significantly different for isolates from the two sampling sites, suggesting that certain strains may be endemic to each sampling site. Not all Rhodopseudomonas palustris isolates could degrade benzoate, a feature that has previously been thought to be characteristic of the species. There were differences in the BOX-PCR genomic fingerprints and restriction fragment length polymorphisms of benzoate-coenzyme A ligase genes and form I and form II ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) genes between benzoate-degrading and non-benzoate-degrading genotypes. The ability to distinguish these two Rhodopseudomonas palustris groups based on multiple genetic differences may reflect an incipient speciation event resulting from adaptive evolution to local environmental conditions.     

Benzoyl Coenzyme A Pathway-Mediated Metabolism of meta-Hydroxy-Aromatic Acids in Rhodopseudomonas palustris

Photoheterotrophic metabolism of two meta-hydroxy-aromatic acids, meta-, para-dihydroxybenzoate (protocatechuate) and meta-hydroxybenzoate, was investigated in Rhodopseudomonas palustris. When protocatechuate was the sole organic carbon source, photoheterotrophic growth in R. palustris was slow relative to cells using compounds known to be metabolized by the benzoyl coenzyme A (benzoyl-CoA) pathway. R. palustris was unable to grow when meta-hydroxybenzoate was provided as a sole source of organic carbon under photoheterotrophic growth conditions. However, in cultures supplemented with known benzoyl-CoA pathway inducers (para-hydroxybenzoate, benzoate, or cyclohexanoate), protocatechuate and meta-hydroxybenzoate were taken up from the culture medium. Further, protocatechuate and meta-hydroxybenzoate were each removed from cultures containing both meta-hydroxy-aromatic acids at equimolar concentrations in the absence of other organic compounds. Analysis of changes in culture optical density and in the concentration of soluble organic compounds indicated that the loss of these meta-hydroxy-aromatic acids was accompanied by biomass production. Additional experiments with defined mutants demonstrated that enzymes known to participate in the dehydroxylation of para-hydroxybenzoyl-CoA (HbaBCD) and reductive dearomatization of benzoyl-CoA (BadDEFG) were required for metabolism of protocatechuate and meta-hydroxybenzoate. These findings indicate that, under photoheterotrophic growth conditions, R. palustris can degrade meta-hydroxy-aromatic acids via the benzoyl-CoA pathway, apparently due to the promiscuity of the enzymes involved.     

Correlation between the production of exopolysaccharides and oxalic acid secretion by Ganoderma applanatum and Tyromyces palustris

The secretion of exopolysaccharides and oxalic acid in cultures of a white rot Ganoderma applanatum strain and a brown rot Tyromyces palustris strain were tested in terms of culture time, pH range, and temperature. The high yield of exopolysaccharides (EPS) required a moderate temperature of 28 °C for G. applanatum and 20 °C for T. palustris. G. applanatum and T. palustris accumulated more EPS when the concentration of the carbon source (maltose for G. applanatum and fructose for T. palustris) was 30 g/L. The results indicate that the production of oxalic acid by G. applanatum is correlated with the initial pH value of the culture medium and the concentration of oxalic acid increased to 1.66 ± 0.2 mM at the initial pH of 6.5 during the fungal growth. During the growth of T. palustris, the reduction of the initial pH value of the growing medium lowered the oxalic acid concentration from 7.7 ± 0.6 mM at pH 6.0 to 1.99 ± 0.2 mM at pH 3.5. T. palustris accumulated considerably more oxalic acid than G. applanatum and its presence did not affect significantly the production of exopolysaccharides. We also observed that the maximum amounts of exopolysaccharides secreted during cultivation of G. applanatum and T. palustris were 45.8 ± 1.2 and 19.1 ± 1.2 g/L, respectively.     

Zur phytozönologischen Bewertung der Feuchtwiesen mitCirsium palustre in Nordwestböhmen

Auf Grund der pflanzensoziologischen Materiale aus NW-Böhmen wurde eine neueCalthion-Assoziation, u. zw. dasPolygono-Cirsietum palustris beschrieben. Diese Assoziation ist in Böhmen und W-Mähren vorwiegend an höhere Lagen der aus Gesteinen des Kristallinikums gebildeten herzynischen Gebirge gebunden. In niedrigeren Lagen kommt es unter analogen Bedingungen oft zur Ausbildung desAngelico-Cirsietum palustris Darimont 1941. Syngenetisch knüpft dasPolygono-Cirsietum palustris an die Nasswiesen (Carici-Agrostetum Oberd. 1951 undPediculari-Juncetum filiformis Preisg. apud Tx. 1947) an. Es handelt sich wohl um eine geographische Vikariante der aus NW-Europa beschriebenenBromus racemosus-Senecio aquaticus Ass. Tx. in Tx. etPrsg. 1951.     

Structure of the natural transgene PgiC2 in the common grass Festuca ovina

Background

A horizontal gene transfer has brought an active nuclear gene, PgiC2, from a polyploid Poa species (P. palustris or a close relative) into the common grass sheep''s fescue (Festuca ovina). The donor and the receptor species are strictly reproductively separated, and PgiC2 occurs in a polymorphic state within F. ovina. The active gene copy is normally closely linked to a very similar pseudogene.

Methodology/Principal Findings

By genome walking we have obtained the up- and downstream sequences of PgiC2 and of corresponding genes in the donor and recipient species. Comparisons of these sequences show that the complete upstream region necessary for the gene''s expression is included in the transferred segment. About 1 kb upstream of PgiC2 a fragment with transposition associated properties has been found (TAF). It is present in P. palustris and its polyploid relatives, though not at the homologous position, and is absent from many other grasses, including non-transgenic F. ovina plants. It is possible that it is a part of a transposing element involved in getting the gene into a transferring agent and/or into the recipient chromosome.

Conclusions/Significance

The close similarity of the up- and downstream regions with the corresponding regions in P. palustris excludes all suggestions that PgiC2 is not a HGT but the result of a duplication within the F. ovina lineage. The small size of the genetic material transferred, the complex nature of the PgiC2 locus, and the associated fragment with transposition associated properties suggest that the horizontal transfer occurred via a vector and not via illegitimate pollination.     

Experimental predation studies of malacophagous larvae of Sepedon fuscipennis (Diptera: Sciomyzidae) and aquatic snails

Experimental studies were conducted under both laboratory and field conditions to determine the effects of prey density, three levels of prey aggregation, water depth, and predator density on the number of snails killed per larva of Sepedon fuscipennis. Of these factors, predation rates were most influenced by prey density and water depth. The number of small (2–4.5 mm) Lymnaea palustris killed per larva of S. fuscipennis increased at a decreasing rate as prey density increased under shallow water conditions. Larvae killed a mean of 14 snails at a prey density of 200/m², while an average of 24 snails were killed per larva of S. fuscipennis at a prey density of 4000/m². This functional response to prey density was largely confined to third-instar larvae, and as water depth was increased the response was not apparent.A field study in which larval densities of S. fuscipennis were manipulated showed that the population density of smaller individuals of L. palustris (< 4.5 mm) was reduced when predator density was increased. Populations of Physa integra, Gyraulus parvus, and larger L. palustris were not significantly reduced by the malacophagous larvae at the levels tested.