scholarly journals Biodiversity of Algae and Cyanobacteria in Biological Soil Crusts Collected Along a Climatic Gradient in Chile Using an Integrative Approach

2020 ◽  
Vol 8 (7) ◽  
pp. 1047 ◽  
Author(s):  
Elena Samolov ◽  
Karen Baumann ◽  
Burkhard Büdel ◽  
Patrick Jung ◽  
Peter Leinweber ◽  
...  
Keyword(s):  
Species Richness ◽  
Coniferous Forest ◽  
Its Region ◽  
Small Subunit ◽  
Dry Forest ◽  
Temperate Climate ◽  
Integrative Approach ◽  
Small Subunit Rrna ◽  
Forest Region ◽  
Eukaryotic Microorganisms

Biocrusts are associations of various prokaryotic and eukaryotic microorganisms in the top millimeters of soil, which can be found in every climate zone on Earth. They stabilize soils and introduce carbon and nitrogen into this compartment. The worldwide occurrence of biocrusts was proven by numerous studies in Europe, Africa, Asia and North America, leaving South America understudied. Using an integrative approach, which combines morphological and molecular characters (small subunit rRNA and ITS region), we examined the diversity of key biocrust photosynthetic organisms at four sites along the latitudinal climate gradient in Chile. The most northern study site was located in the Atacama Desert (arid climate), followed by open shrubland (semiarid climate), a dry forest region (Mediterranean climate) and a mixed broad leaved-coniferous forest (temperate climate) in the south. The lowest species richness was recorded in the desert (18 species), whereas the highest species richness was observed in the Mediterranean zone (40 species). Desert biocrusts were composed exclusively of single-celled Chlorophyta algae, followed by cyanobacteria. Chlorophyta, Streptophyta and cyanobacteria dominated semiarid biocrusts, whereas Mediterranean and temperate Chilean biocrusts were composed mostly of Chlorophyta, Streptophyta and Ochrophyta. Our investigation of Chilean biocrust suggests high biodiversity of South American biocrust phototrophs.

Dry forests of the Galápagos: a comparative assessment of a World Heritage Site

2020 ◽  
Vol 26 (2) ◽  
pp. 161
Author(s):  
Thomas W. Gillespie ◽  
Gunnar Keppel ◽  
Chelsea M. Robinson ◽  
Gonzalo Rivas-Torres
Keyword(s):  
Species Richness ◽  
Woody Plants ◽  
Native Species ◽  
Forest Cover ◽  
Conservation Status ◽  
Dry Forest ◽  
World Heritage Site ◽  
Dry Forests ◽  
Forest Region ◽  
The Pacific

Despite worldwide knowledge of the importance of the Galápagos archipelago, there is little comparative plot data from the forests in the dry regions. We examined patterns of woody plant (≥2.5cm diameter at breast height (DBH)) species richness and structure using Gentry’s transect method (0.1ha) on the three largest islands in the Galápagos. We identified the conservation status of woody plants within the dry forest region, assessed forest cover and change in the region, and compared field results to other tropical dry forests in the Pacific. Of the 22 species encountered (11 native, 11 endemic), there were no non-native species and only one threatened species. Isabela, Santa Cruz and San Cristóbal have similar overall levels of species, genera, family and liana richness per site, but significantly different tree species richness, density and tree height per transect. Geospatial databases identified 51 species (native 40%, endemic 60%) of woody plants (≥2.5cm DBH) within the dry forest region of the Galápagos and 13 species (10 from the genus Scalesia) on the IUCN Red List. There is an estimated 551.97km2 of dry forest in the Galápagos and there has been little change (<0.01%) in forest cover from 2000 to 2015. Dry forests of the Galápagos have similar levels of species richness to Hawaii and the Marquesas but contain lower densities, basal areas and tree heights than other dry forests in the Pacific. These dry forests appear to be the best preserved and protected tropical dry forest in the Pacific.

Analysis of the ITS region and partial ssu and lsu rRNA genes ofBlastocystisandProteromonas lacertae

Parasitology ◽  
2005 ◽  
Vol 131 (2) ◽  
pp. 187-196 ◽  
Author(s):  
J. D. HOEVERS ◽  
K. F. SNOWDEN
Keyword(s):  
Large Subunit ◽  
Geographic Origin ◽  
Its Region ◽  
Small Subunit ◽  
Rdna Sequence ◽  
Rrna Genes ◽  
Small Subunit Rrna ◽  
Chattonella Marina ◽  
Internal Transcribed Spacer Region ◽  
Cylindrotheca Closterium

Blastocystisis a common single-celled enteric parasite found in a large variety of hosts. Recent molecular analysis supports the concept that this eukaryotic organism is a stramenopile most closely related toProteromonas lacertae, a parasite of reptiles. In this study, the internal transcribed spacer region, partial small subunit rRNA and large subunit rRNA genes from 7Blastocystisisolates (5 human, 1 pig and 1 sheep), and aProteromonas lacertaeisolate were amplified by PCR, cloned and sequenced.Blastocystiswas found to be a typical eukaryote with both ITS1 and ITS2 regions present. Phylogenetic analysis based on the entire PCR amplicon revealed that theBlastocystisisolates did not segregate according to host or geographic origin. The highest sequence identities with the conservedBlastocystis5·8S rDNA sequence were with the stramenopilesFibrocapsa japonica,Chattonella marina,Cylindrotheca closteriumandHyphochytrium catenoides. The most parsimonious tree based on the 5·8S rDNA sequence fromP. lacertae, 11 other stramenopiles, 2 fungi, 3 algae and 3 alveolates showedBlastocystispositioned within the stramenopiles, withP. lacertaeas its closest relative. This work therefore supports the hypothesis thatBlastocystisis most closely related toP. lacertae, and that it should be regarded as an unusual stramenopile.

scholarly journals Taxonomy, Ontogenesis and Evolutionary Relationships of the Algae-Bearing Ciliate Bourlandella viridis (Kahl, 1932) comb. nov., With Establishment of a New Genus and New Family (Protista, Ciliophora, Hypotrichia)

2021 ◽  
Vol 11 ◽  
Author(s):  
Wenya Song ◽  
Tengyue Zhang ◽  
Xue Zhang ◽  
Alan Warren ◽  
Weibo Song ◽  
...  
Keyword(s):  
New Genus ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
New Combination ◽  
Integrative Approach ◽  
Rrna Gene ◽  
Intermediate Form ◽  
Small Subunit Rrna ◽  
New Family ◽  
Wide Range

Hypotrichs are the most complex and highly differentiated ciliate lineages and have great potential for evolutionary novelties. Problems in hypotrich systematics are mainly due to discordance between the morphological and genetic data (mainly small subunit rRNA gene). Species with morphologies that are characteristic of two or more higher rank taxa are probably a major contributing factor to these conflicts. The present study describes a Chinese population of a poorly known organism with numerous endosymbiotic zoochlorellae, the morphology of which corresponds well with the type population of Limnoholosticha viridis (Kahl, 1932) Li et al., 2017. Newly obtained information shows this species has a zigzag midventral cirral pattern that is diagnostic of urostylids, whereas the dorsal ciliature shares features (presence of dorsomarginal kinety and dorsal kinety 3 fragmentation) that are typical of oxytrichids. Molecular phylogenetic analyses reveal a close relationship with oxytrichids. An integrative approach combining morphological, morphogenetic, phylogenetic and ecological analyses indicates that L. viridis represents a new genus and new family which might be an intermediate form between uorstylids and dorsomarginalians. Thus, Bourlandellidae fam. nov. and Bourlandella gen. nov. are here established. Lastly, we speculate that phenotypic convergence and mixtrophy might confer on the new combination, Bourlandella viridis (Kahl, 1932) comb. nov., the ability to adapt to a wide range of environmental conditions.

scholarly journals Targeted Next-Generation Sequencing and Informatics as an Effective Tool to Establish the Composition of Bovine Piroplasm Populations in Endemic Regions

2020 ◽  
Vol 9 (1) ◽  
pp. 21
Author(s):  
Abdul Ghafar ◽  
Anson V. Koehler ◽  
Ross S. Hall ◽  
Charles G. Gauci ◽  
Robin B. Gasser ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Water Buffalo ◽  
Hypervariable Region ◽  
Small Subunit ◽  
Rrna Gene ◽  
Next Generation ◽  
Small Subunit Rrna ◽  
Tropical Theileriosis ◽  
Ecological Zones ◽  
Generation Sequencing

Protists of the genera Babesia and Theileria (piroplasms) cause some of the most prevalent and debilitating diseases for bovines worldwide. In this study, we established and used a next-generation sequencing-informatic approach to explore the composition of Babesia and Theileria populations in cattle and water buffalo in a country (Pakistan) endemic for these pathogens. We collected individual blood samples from cattle (n = 212) and water buffalo (n = 154), extracted genomic DNAs, PCR-amplified the V4 hypervariable region of 18S small subunit rRNA gene from piroplasms, sequenced amplicons using Illumina technology, and then analysed data using bioinformatic platforms. The results revealed piroplasms in 68.9% (252/366) samples, with overall occurrence being markedly higher in cattle (85.8%) than in water buffaloes (45.5%). Babesia (B.) occultans and Theileria (T.) lestoquardi-like species were recorded for the first time in Pakistan, and, overall, T. annulata was most commonly detected (65.8%) followed by B. bovis (7.1%), B. bigemina (4.4%), and T. orientalis (0.5%), with the genetic variability within B. bovis being pronounced. The occurrence and composition of piroplasm species varied markedly across different agro-ecological zones. The high detection of T. annulata in asymptomatic animals suggested a relatively high level of endemic stability of tropical theileriosis in the bovine population.

scholarly journals Comparative Sequence Analysis and Patterns of Covariation in RNA Secondary Structures

Genetics ◽  
2000 ◽  
Vol 154 (2) ◽  
pp. 909-921 ◽  
Author(s):  
John Parsch ◽  
John M Braverman ◽  
Wolfgang Stephan
Keyword(s):  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Rnase P ◽  
Secondary Structures ◽  
Comparative Sequence Analysis ◽  
Small Subunit ◽  
Physical Parameters ◽  
Small Subunit Rrna ◽  
Base Pairing ◽  
Compensatory Evolution

Abstract A novel method of RNA secondary structure prediction based on a comparison of nucleotide sequences is described. This method correctly predicts nearly all evolutionarily conserved secondary structures of five different RNAs: tRNA, 5S rRNA, bacterial ribonuclease P (RNase P) RNA, eukaryotic small subunit rRNA, and the 3′ untranslated region (UTR) of the Drosophila bicoid (bcd) mRNA. Furthermore, covariations occurring in the helices of these conserved RNA structures are analyzed. Two physical parameters are found to be important determinants of the evolution of compensatory mutations: the length of a helix and the distance between base-pairing nucleotides. For the helices of bcd 3′ UTR mRNA and RNase P RNA, a positive correlation between the rate of compensatory evolution and helix length is found. The analysis of Drosophila bcd 3′ UTR mRNA further revealed that the rate of compensatory evolution decreases with the physical distance between base-pairing residues. This result is in qualitative agreement with Kimura's model of compensatory fitness interactions, which assumes that mutations occurring in RNA helices are individually deleterious but become neutral in appropriate combinations.

scholarly journals Culture-Independent Analysis of Indomethacin-Induced Alterations in the Rat Gastrointestinal Microbiota

2006 ◽  
Vol 72 (10) ◽  
pp. 6707-6715 ◽  
Author(s):  
Andrew B. Dalby ◽  
Daniel N. Frank ◽  
Allison L. St. Amand ◽  
Alison M. Bendele ◽  
Norman R. Pace
Keyword(s):  
Small Intestine ◽  
Lymph Nodes ◽  
Small Subunit ◽  
Rrna Genes ◽  
Small Subunit Rrna ◽  
Mesenteric Lymph Nodes ◽  
Gastrointestinal Microbiota ◽  
Mesenteric Lymph ◽  
Independent Analysis ◽  
Culture Independent

ABSTRACT Nonsteroidal anti-inflammatory drugs (NSAIDs) are commonly prescribed for a variety of inflammatory conditions; however, the benefits of this class of drugs are accompanied by deleterious side effects, most commonly gastric irritation and ulceration. NSAID-induced ulceration is thought to be exacerbated by intestinal microbiota, but previous studies have not identified specific microbes that contribute to these adverse effects. In this study, we conducted a culture-independent analysis of ∼1,400 bacterial small-subunit rRNA genes associated with the small intestines and mesenteric lymph nodes of rats treated with the NSAID indomethacin. This is the first molecular analysis of the microbiota of the rat small intestine. A comparison of clone libraries and species-specific quantitative PCR results from rats treated with indomethacin and untreated rats revealed that organisms closely related to Enterococcus faecalis were heavily enriched in the small intestine and mesenteric lymph nodes of the treated rats. These data suggest that treatment of NSAID-induced ulceration may be facilitated by addressing the microbiological imbalances.

scholarly journals Specificity of Associations between Bacteria and the Coral Pocillopora meandrina during Early Development

2012 ◽  
Vol 78 (20) ◽  
pp. 7467-7475 ◽  
Author(s):  
Amy Apprill ◽  
Heather Q. Marlow ◽  
Mark Q. Martindale ◽  
Michael S. Rappé
Keyword(s):  
Small Subunit ◽  
Rrna Genes ◽  
Polymorphism Analysis ◽  
Roseobacter Clade ◽  
Small Subunit Rrna ◽  
Content Type ◽  
Sterile Seawater ◽  
Show Evidence ◽  
Coral Health

ABSTRACTRelationships between corals and specific bacterial associates are thought to play an important role in coral health. In this study, the specificity of bacteria associating with the coralPocillopora meandrinawas investigated by exposing coral embryos to various strains of cultured marine bacteria, sterile seawater, or raw seawater and examining the identity, density, and location of incorporated cells. The isolates utilized in this experiment included members of the Roseobacter and SAR11 clades of theAlphaproteobacteria, aPseudoalteromonasspecies of theGammaproteobacteria, and aSynechococcusspecies of theCyanobacteriaphylum. Based on terminal restriction fragment length polymorphism analysis of small-subunit rRNA genes, similarities in bacterial communities associated with 170-h-old planulae were observed regardless of treatment, suggesting that bacteria may have been externally associated from the outset of the experiment. Microscopic examination ofP. meandrinaplanulae by fluorescencein situhybridization with bacterial and Roseobacter clade-specific oligonucleotide probes revealed differences in the densities and locations of planulae-associated cells. Planulae exposed to either raw seawater or strains ofPseudoalteromonasand Roseobacter harbored the highest densities of internally associated cells, of which 20 to 100% belonged to the Roseobacter clade. Planulae exposed to sterile seawater or strains of the SAR11 clade andSynechococcusdid not show evidence of prominent bacterial associations. Additional analysis of the raw-seawater-exposed planulae via electron microscopy confirmed the presence of internally associated prokaryotic cells, as well as virus-like particles. These results suggest that the availability of specific microorganisms may be an important factor in the establishment of coral-bacterial relationships.

scholarly journals First Report of Dollar Spot of Sandbur Caused by Sclerotinia homoeocarpa in Oklahoma

Plant Disease ◽  
2014 ◽  
Vol 98 (8) ◽  
pp. 1160-1160
Author(s):  
F. Flores ◽  
N. R. Walker
Keyword(s):  
Warm Season ◽  
Its Region ◽  
Small Subunit ◽  
Type I ◽  
Academic Press ◽  
Sclerotinia Homoeocarpa ◽  
Dollar Spot ◽  
First Report ◽  
Small Subunit Rdna ◽  
Disturbed Soils

Sandbur (Cenchrus incertus Curtis) is a warm-season, annual, noxious, grassy weed native to southern North America. It is common in sandy, disturbed soils and can also be found in home lawns and sport fields where low turf density facilitates its establishment. In July 2013, after a period of frequent rainfall and heavy dew, symptoms of dollar spot-like lesions (1) were observed on sandbur plants growing in a mixed stand of turf-type and native warm-season grasses in Logan County, Oklahoma. Lesions, frequently associated with leaf sheaths, were tan and surrounded by a dark margin. Symptomatic leaves were surface sterilized and plated on potato dextrose agar amended with 10 ppm rifampicin, 250 ppm ampicillin, and 5 ppm fenpropathrin. After incubation, a fungus morphologically identical to Sclerotinia homoeocarpa Bennett was consistently isolated. The nuclear ribosomal internal transcribed spacer (ITS) region of two different isolates, SCL2 and SCL3, were amplified using primers ITS4 and ITS5 (2). The DNA products were sequenced and BLAST analyses were used to compare sequences with those in GenBank. The sequence for isolate SLC2 was 869 bp, contained a type I intron in the 18S small subunit rDNA, and was identical to accession EU123803. The ITS sequence for isolate SLC3 was 535 bp and identical to accession EU123802. Twenty-five-day-old seedlings of C. incertus were inoculated by placing 5-mm-diameter agar plugs, colonized by mycelia of each S. homoeocarpa isolate, onto two of the plants' leaves. Plugs were held in place with Parafilm. Two plants were inoculated with each isolate and sterile agar plugs were placed on two leaves of another seedling as control. Plants were incubated in a dew chamber at 20°C and a 12-h photoperiod. After 3 days of incubation, water-soaked lesions surrounded by a dark margin appeared on inoculated plants only. Fungi that were later identified as S. homoeocarpa isolates SLC2 and SLC3 by sequencing of the ITS region were re-isolated from symptomatic leaves, fulfilling Koch's postulates. To our knowledge, this is the first report of dollar spot on sandbur. References: (1) R. W. Smiley et al. Page 22 in: Compendium of Turfgrass Diseases. 3rd ed. The American Phytopathological Society, St. Paul, MN, 2005. (2) T. J. White et al. Page 315 in: PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, CA, 1990.

scholarly journals Phytoplankton distribution patterns in the northwestern Sargasso Sea revealed by small subunit rRNA genes from plastids

2011 ◽  
Vol 6 (3) ◽  
pp. 481-492 ◽  
Author(s):  
Alexander H Treusch ◽  
Elif Demir-Hilton ◽  
Kevin L Vergin ◽  
Alexandra Z Worden ◽  
Craig A Carlson ◽  
...  
Keyword(s):  
Distribution Patterns ◽  
Small Subunit ◽  
Rrna Genes ◽  
Sargasso Sea ◽  
Small Subunit Rrna ◽  
Phytoplankton Distribution
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