Genome-Directed Isolation of the Key Nitrogen Fixer Leptospirillum ferrodiazotrophum sp. nov. from an Acidophilic Microbial Community

ABSTRACT Analysis of assembled random shotgun sequence data from a low-diversity, subsurface acid mine drainage (AMD) biofilm revealed a single nif operon. This was found on a genome fragment belonging to a member of Leptospirillum group III, a lineage in the Nitrospirae phylum with no cultivated representatives. Based on the prediction that this organism is solely responsible for nitrogen fixation in the community, we pursued a selective isolation strategy to obtain the organism in pure culture. An AMD biofilm sample naturally abundant in Leptospirillum group III cells was homogenized, filtered, and serially diluted into a nitrogen-free liquid medium. The resulting culture in the terminal dilution grew autotrophically to a maximum cell density of ∼106 cells/ml, oxidizing ferrous iron as the sole energy source. 16S rRNA-internal transcribed spacer region clone library analysis confirmed that the isolate is a member of Leptospirillum group III and that the culture is axenic. We propose the name Leptospirillum ferrodiazotrophum sp. nov. for this iron-oxidizing, free-living diazotroph. This study highlights how environmental sequence data can provide insights for culturing previously uncultured microorganisms.

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Barcoding lichen-forming fungi using 454 pyrosequencing is challenged by artifactual and biological sequence variation

Genome ◽

10.1139/gen-2015-0189 ◽

2016 ◽

Vol 59 (9) ◽

pp. 685-704 ◽

Cited By ~ 16

Author(s):

Kristiina Mark ◽

Carolina Cornejo ◽

Christine Keller ◽

Daniela Flück ◽

Christoph Scheidegger

Keyword(s):

454 Pyrosequencing ◽

Ecological Integrity ◽

Common Species ◽

Sequencing Error ◽

Reference Database ◽

Biological Sequence ◽

Internal Transcribed Spacer Region ◽

Epiphytic Lichen ◽

Fungal Partner ◽

A Genome

Although lichens (lichen-forming fungi) play an important role in the ecological integrity of many vulnerable landscapes, only a minority of lichen-forming fungi have been barcoded out of the currently accepted ∼18 000 species. Regular Sanger sequencing can be problematic when analyzing lichens since saprophytic, endophytic, and parasitic fungi live intimately admixed, resulting in low-quality sequencing reads. Here, high-throughput, long-read 454 pyrosequencing in a GS FLX+ System was tested to barcode the fungal partner of 100 epiphytic lichen species from Switzerland using fungal-specific primers when amplifying the full internal transcribed spacer region (ITS). The present study shows the potential of DNA barcoding using pyrosequencing, in that the expected lichen fungus was successfully sequenced for all samples except one. Alignment solutions such as BLAST were found to be largely adequate for the generated long reads. In addition, the NCBI nucleotide database—currently the most complete database for lichen-forming fungi—can be used as a reference database when identifying common species, since the majority of analyzed lichens were identified correctly to the species or at least to the genus level. However, several issues were encountered, including a high sequencing error rate, multiple ITS versions in a genome (incomplete concerted evolution), and in some samples the presence of mixed lichen-forming fungi (possible lichen chimeras).

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Nucleotide sequences of highly repeated DNAs; compilation and comments

Genetics Research ◽

10.1017/s0016672300020711 ◽

1982 ◽

Vol 39 (1) ◽

pp. 1-30 ◽

Cited By ~ 33

Author(s):

George L. Gabor Miklos ◽

Amanda Clare Gill

Keyword(s):

Satellite Dna ◽

Germ Line ◽

Sequence Data ◽

Allelic Variation ◽

Neutral Theory ◽

Natural Populations ◽

Evolutionary Significance ◽

Nucleotide Sequence Data ◽

A Genome ◽

Repeated Dnas

SummaryThe nucleotide sequence data from highly repeated DNAs of inverte-brates and mammals are summarized and briefly discussed. Very similar conclusions can be drawn from the two data bases. Sequence complexities can vary from 2 bp to at least 359 bp in invertebrates and from 3 bp to at least 2350 bp in mammals. The larger sequences may or may not exhibit a substructure. Significant sequence variation occurs for any given repeated array within a species, but the sources of this heterogeneity have not been systematically partitioned. The types of alterations in a basic repeating unit can involve base changes as well as deletions or additions which can vary from 1 bp to at least 98 bp in length. These changes indicate that sequence per se is unlikely to be under significant biological constraints and may sensibly be examined by analogy to Kimura's neutral theory for allelic variation. It is not possible with the present evidence to discriminate between the roles of neutral and selective mechanisms in the evolution of highly repeated DNA.Tandemly repeated arrays are constantly subjected to cycles of amplification and deletion by mechanisms for which the available data stem largely from ribosomal genes. It is a matter of conjecture whether the solutions to the mechanistic puzzles involved in amplification or rapid redeployment of satellite sequences throughout a genome will necessarily give any insight into biological functions.The lack of significant somatic effects when the satellite DNA content of a genome is significantly perturbed indicates that the hunt for specific functions at the cellular level is unlikely to prove profitable.The presence or in some cases the amount of satellite DNA on a chromosome, however, can have significant effects in the germ line. There the data show that localized condensed chromatin, rich in satellite DNA, can have the effect of rendering adjacent euchromatic regions rec−, or of altering levels of recombination on different chromosomes. No data stemming from natural populations however are yet available to tell us if these effects are of adaptive or evolutionary significance.

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Transcriptome analysis ofSchistosoma mansonilarval development using serial analysis of gene expression (SAGE)

Parasitology ◽

10.1017/s0031182009005733 ◽

2009 ◽

Vol 136 (5) ◽

pp. 469-485 ◽

Cited By ~ 22

Author(s):

A. S. TAFT ◽

J. J. VERMEIRE ◽

J. BERNIER ◽

S. R. BIRKELAND ◽

M. J. CIPRIANO ◽

...

Keyword(s):

Gene Expression ◽

Sequence Data ◽

Subsequent Development ◽

Differentially Expressed ◽

Cdna Libraries ◽

Genome Wide ◽

A Genome ◽

Genome Wide Expression ◽

Cell Conditioned Medium

SUMMARYInfection of the snail,Biomphalaria glabrata, by the free-swimming miracidial stage of the human blood fluke,Schistosoma mansoni, and its subsequent development to the parasitic sporocyst stage is critical to establishment of viable infections and continued human transmission. We performed a genome-wide expression analysis of theS. mansonimiracidia and developing sporocyst using Long Serial Analysis of Gene Expression (LongSAGE). Five cDNA libraries were constructed from miracidia andin vitrocultured 6- and 20-day-old sporocysts maintained in sporocyst medium (SM) or in SM conditioned by previous cultivation with cells of theB. glabrataembryonic (Bge) cell line. We generated 21 440 SAGE tags and mapped 13 381 to theS. mansonigene predictions (v4.0e) either by estimating theoretical 3′ UTR lengths or using existing 3′ EST sequence data. Overall, 432 transcripts were found to be differentially expressed amongst all 5 libraries. In total, 172 tags were differentially expressed between miracidia and 6-day conditioned sporocysts and 152 were differentially expressed between miracidia and 6-day unconditioned sporocysts. In addition, 53 and 45 tags, respectively, were differentially expressed in 6-day and 20-day cultured sporocysts, due to the effects of exposure to Bge cell-conditioned medium.

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Deep learning predicts short non-coding RNA functions from only raw sequence data

PLoS Computational Biology ◽

10.1371/journal.pcbi.1008415 ◽

2020 ◽

Vol 16 (11) ◽

pp. e1008415

Author(s):

Teresa Maria Rosaria Noviello ◽

Francesco Ceccarelli ◽

Michele Ceccarelli ◽

Luigi Cerulo

Keyword(s):

Secondary Structure ◽

Sequence Data ◽

Computational Cost ◽

Large Data ◽

Sequence Information ◽

Structure Information ◽

Non Coding Rna ◽

A Genome ◽

Data Volume ◽

Biological Functionality

Small non-coding RNAs (ncRNAs) are short non-coding sequences involved in gene regulation in many biological processes and diseases. The lack of a complete comprehension of their biological functionality, especially in a genome-wide scenario, has demanded new computational approaches to annotate their roles. It is widely known that secondary structure is determinant to know RNA function and machine learning based approaches have been successfully proven to predict RNA function from secondary structure information. Here we show that RNA function can be predicted with good accuracy from a lightweight representation of sequence information without the necessity of computing secondary structure features which is computationally expensive. This finding appears to go against the dogma of secondary structure being a key determinant of function in RNA. Compared to recent secondary structure based methods, the proposed solution is more robust to sequence boundary noise and reduces drastically the computational cost allowing for large data volume annotations. Scripts and datasets to reproduce the results of experiments proposed in this study are available at: https://github.com/bioinformatics-sannio/ncrna-deep.

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First Report of a Leaf Spot Disease of Bells-of-Ireland (Moluccella laevis) Caused by Cercospora apii in California

Plant Disease ◽

10.1094/pdis.2003.87.2.203a ◽

2003 ◽

Vol 87 (2) ◽

pp. 203-203

Author(s):

S. T. Koike ◽

S. A. Tjosvold ◽

J. Z. Groenewald ◽

P. W. Crous

Keyword(s):

Leaf Spot ◽

Sequence Data ◽

Disease Incidence ◽

Leaf Spot Disease ◽

Conidial Suspension ◽

Internal Transcribed Spacer Region ◽

First Report ◽

Spot Disease ◽

Leaf Spots ◽

Initial Symptoms

Bells-of-Ireland (Moluccella laevis) (Lamiaceae) is an annual plant that is field planted in coastal California (Santa Cruz County) for commercial cutflower production. In 2001, a new leaf spot disease was found in these commercially grown cutflowers. The disease was most serious in the winter-grown crops in 2001 and 2002, with a few plantings having as much as 100% disease incidence. All other plantings that were surveyed during this time had at least 50% disease. Initial symptoms consisted of gray-green leaf spots. Spots were generally oval in shape, often delimited by the major leaf veins, and later turned tan. Lesions were apparent on both adaxial and abaxial sides of the leaves. A cercosporoid fungus having fasciculate conidiophores, which formed primarily on the abaxial leaf surface, was consistently associated with the spots. Based on morphology and its host, this fungus was initially considered to be Cercospora molucellae Bremer & Petr., which was previously reported on leaves of M. laevis in Turkey (1). However, sequence data obtained from the internal transcribed spacer region (ITS1, ITS2) and the 5.8S gene (STE-U 5110, 5111; GenBank Accession Nos. AY156918 and AY156919) indicated there were no base pair differences between the bells-of-Ireland isolates from California, our own reference isolates of C. apii, as well as GenBank sequences deposited as C. apii. Based on these data, the fungus was subsequently identified as C. apii sensu lato. Pathogenicity was confirmed by spraying a conidial suspension (1.0 × 105 conidia/ml) on leaves of potted bells-of-Ireland plants, incubating the plants in a dew chamber for 24 h, and maintaining them in a greenhouse (23 to 25°C). After 2 weeks, all inoculated plants developed leaf spots that were identical to those observed in the field. C. apii was again associated with all leaf spots. Control plants, which were treated with water, did not develop any symptoms. The test was repeated and the results were similar. To our knowledge this is the first report of C. apii as a pathogen of bells-of-Ireland in California. Reference: (1) C. Chupp. A Monograph of the Fungus Genus Cercospora. Cornell University Press, Ithaca, New York, 1954.

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Factors mediating plastid dependency and the origins of parasitism in apicomplexans and their close relatives

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1423790112 ◽

2015 ◽

Vol 112 (33) ◽

pp. 10200-10207 ◽

Cited By ~ 117

Author(s):

Jan Janouškovec ◽

Denis V. Tikhonenkov ◽

Fabien Burki ◽

Alexis T. Howe ◽

Martin Kolísko ◽

...

Keyword(s):

Plastid Genome ◽

Sequence Data ◽

Sister Group ◽

Molecular Characteristics ◽

Phylogenomic Analysis ◽

Free Living ◽

Plastid Genomes ◽

Monophyletic Lineage ◽

Causative Agents ◽

Close Relatives

Apicomplexans are a major lineage of parasites, including causative agents of malaria and toxoplasmosis. How such highly adapted parasites evolved from free-living ancestors is poorly understood, particularly because they contain nonphotosynthetic plastids with which they have a complex metabolic dependency. Here, we examine the origin of apicomplexan parasitism by resolving the evolutionary distribution of several key characteristics in their closest free-living relatives, photosynthetic chromerids and predatory colpodellids. Using environmental sequence data, we describe the diversity of these apicomplexan-related lineages and select five species that represent this diversity for transcriptome sequencing. Phylogenomic analysis recovered a monophyletic lineage of chromerids and colpodellids as the sister group to apicomplexans, and a complex distribution of retention versus loss for photosynthesis, plastid genomes, and plastid organelles. Reconstructing the evolution of all plastid and cytosolic metabolic pathways related to apicomplexan plastid function revealed an ancient dependency on plastid isoprenoid biosynthesis, predating the divergence of apicomplexan and dinoflagellates. Similarly, plastid genome retention is strongly linked to the retention of two genes in the plastid genome, sufB and clpC, altogether suggesting a relatively simple model for plastid retention and loss. Lastly, we examine the broader distribution of a suite of molecular characteristics previously linked to the origins of apicomplexan parasitism and find that virtually all are present in their free-living relatives. The emergence of parasitism may not be driven by acquisition of novel components, but rather by loss and modification of the existing, conserved traits.

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A Comparison of CO2 and N2 Foaming Behaviors of PP in a Visualization System

International Polymer Processing ◽

10.1515/ipp-2020-350512 ◽

2020 ◽

Vol 35 (5) ◽

pp. 503-517

Author(s):

Q.-P. Guo ◽

J. Wang ◽

C. B. Park

Keyword(s):

Cell Density ◽

Nucleating Agent ◽

Gas Content ◽

Experimental Conditions ◽

Maximum Cell Density ◽

Visualization System ◽

Cell Nucleation ◽

Processing Strategies ◽

Automotive Parts ◽

Maximum Cell

Abstract Understanding of polypropylene (PP) foaming is critically important to reduce the weight of automotive parts. In this study, we used a batch foaming simulation system with visualization cell, to observe the foaming behaviors of PP that is blown with CO2 and N2 under various experimental conditions. We found that the nucleating agent content, initial temperature, pressure (i. e., gas content), and pressure drop rate during foaming have a significant effect on cell nucleation and cell growth. The cell density and the void fraction of PP foamed with CO2 and N2, respectively, were separately observed and compared. It was found that under the same experimental conditions, the maximum cell density of PP foamed with CO2 was higher than that of PP foamed with N2. However, the maximum cell density of PP foamed with CO2 was determined to be lower than that of PP foamed with N2, when the same gas mole numbers were employed. Based on the experimental results, optimum foaming conditions and effective processing strategies for PP-CO2 system are suggested.

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Amanita mansehraensis, a new species in section Vaginatae from Pakistan

Phytotaxa ◽

10.11646/phytotaxa.409.4.1 ◽

2019 ◽

Vol 409 (4) ◽

pp. 189-201 ◽

Cited By ~ 1

Author(s):

MALKA SABA ◽

DANNY HAELEWATERS ◽

MUHAMMAD FIAZ ◽

ABDUL NASIR KHALID ◽

DONALD H. PFISTER

Keyword(s):

New Species ◽

Ribosomal Rna ◽

Internal Transcribed Spacer ◽

Sequence Data ◽

Large Subunit ◽

Pine Forests ◽

Evolutionary Relationships ◽

Internal Transcribed Spacer Region ◽

Bayesian Inferences ◽

A New Species

A new species of Amanita subgenus Amanita sect. Vaginatae is described and illustrated based on material collected in pine forests in district Mansehra, Khyber Pakhtoonkhaw, Pakistan. Amanita mansehraensis is recognized by the presence of a light brown or light greyish olive pileus with strong brown or deep brown pileus center; non-appendiculate, rimose, sulcate or plicate striate pileus margin; subglobose to ellipsoid basidiospores; and a saccate volva. The internal transcribed spacer region (ITS) and large subunit of the nuclear ribosomal RNA gene (nrLSU) were used for the delimitation of this species based on sequence data. The evolutionary relationships of A. mansehraensis with other species of Amanita were inferred by means of Maximum Likelihood and Bayesian inferences of the nrLSU dataset and concatenated ITS+nrLSU dataset. Amanita mansehraensis is most closely related to A. brunneofuliginea, A. pseudovaginata, and the recently described A. glarea.

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Genome Sequence of Pseudomonas sp. Strain AN3A02, Isolated from Rhizosphere of Deschampsia antarctica Desv., with Antagonism against Botrytis cinerea

Microbiology Resource Announcements ◽

10.1128/mra.00320-20 ◽

2020 ◽

Vol 9 (21) ◽

Author(s):

Matías Poblete-Morales ◽

Claudia Rabert ◽

Andrés F. Olea ◽

Héctor Carrasco ◽

Raúl Calderón ◽

...

Keyword(s):

Botrytis Cinerea ◽

Genome Sequence ◽

Sequence Data ◽

Draft Genome ◽

Draft Genome Sequence ◽

Deschampsia Antarctica ◽

Dual Culture ◽

Content Type ◽

A Genome ◽

Antarctic Continent

ABSTRACT Here, we announce the draft genome sequence of Pseudomonas sp. strain AN3A02, isolated from the rhizosphere of one of the only two species of vascular plants existing in the Antarctic continent, Deschampsia antarctica Desv. This isolate, which inhibited the mycelial growth of Botrytis cinerea in dual culture, has a genome sequence of 6,778,644 bp, with a G+C content of 60.4%. These draft genome sequence data provide insight into the genetics underpinning the antifungal activity of this strain.

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Phylogeny, Distribution, and Pathogenicity of Lasiodiplodia Species Associated With Cankers and Dieback Symptoms of Persian Lime in Mexico

Plant Disease ◽

10.1094/pdis-06-18-1036-re ◽

2019 ◽

Vol 103 (6) ◽

pp. 1156-1165 ◽

Cited By ~ 3

Author(s):

M. A. Bautista-Cruz ◽

G. Almaguer-Vargas ◽

S. G. Leyva-Mir ◽

M. T. Colinas-León ◽

K. C. Correia ◽

...

Keyword(s):

Sequence Data ◽

Elongation Factor ◽

Internal Transcribed Spacer Region ◽

Translation Elongation ◽

Dna Sequence Data ◽

Tubulin Genes ◽

Fungal Identification ◽

Mycelial Plug ◽

Inference Methods ◽

Stem Cankers

Persian lime (Citrus latifolia Tan.) is an important and widely cultivated fruit crop in several regions of Mexico. In recent years, severe symptoms of gummosis, stem cankers, and dieback were detected in the Persian lime-producing region in the states of Veracruz and Puebla, Mexico. The aims of this study were to identify the species of Lasiodiplodia associated with these symptoms, determine the distribution of these species, and test their pathogenicity and virulence on Persian lime plants. In 2015, symptomatic samples were collected from 12 commercial Persian lime orchards, and 60 Lasiodiplodia isolates were obtained. Fungal identification of 32 representative isolates was performed using a phylogenetic analysis based on DNA sequence data of the internal transcribed spacer region and part of the translation elongation factor 1-α and β-tubulin genes. Sequence analyses were carried out using the Maximum Likelihood and Bayesian Inference methods. Six Lasiodiplodia species were identified as Lasiodiplodia pseudotheobromae, Lasiodiplodia theobromae, Lasiodiplodia brasiliense, Lasiodiplodia subglobosa, Lasiodiplodia citricola, and Lasiodiplodia iraniensis. All Lasiodiplodia species of this study are reported for the first time in association with Persian lime in Mexico and worldwide. L. pseudotheobromae (46.9% of isolates) was the most frequently isolated species followed by L. theobromae (28.1%) and L. brasiliense (12.5%). Pathogenicity on Persian lime young plants using a mycelial plug inoculation method showed that all identified Lasiodiplodia species were able to cause necrotic lesions and gummosis, but L. subglobosa, L. iraniensis, and L. pseudotheobromae were the most virulent.

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