scholarly journals The Biodiversity and Geochemistry of Cryoconite Holes in Queen Maud Land, East Antarctica

2019 ◽  
Vol 7 (6) ◽  
pp. 160 ◽  
Author(s):  
Stefanie Lutz ◽  
Lori A. Ziolkowski ◽  
Liane G. Benning
Keyword(s):  
High Throughput Sequencing ◽  
Geographic Location ◽  
Carbon Accumulation ◽  
The Arctic ◽  
Rrna Genes ◽  
Geochemical Data ◽  
Eukaryotic Community ◽  
Continental Antarctica ◽  
18S Rrna Genes ◽  
First Time

Cryoconite holes are oases of microbial diversity on ice surfaces. In contrast to the Arctic, where during the summer most cryoconite holes are ‘open’, in Continental Antarctica they are most often ‘lidded’ or completely frozen year-round. Thus, they represent ideal systems for the study of microbial community assemblies as well as carbon accumulation, since individual cryoconite holes can be isolated from external inputs for years. Here, we use high-throughput sequencing of the 16S and 18S rRNA genes to describe the bacterial and eukaryotic community compositions in cryoconite holes and surrounding lake, snow, soil and rock samples in Queen Maud Land. We cross correlate our findings with a broad range of geochemical data including for the first time 13C and 14C analyses of Antarctic cryoconites. We show that the geographic location has a larger effect on the distribution of the bacterial community compared to the eukaryotic community. Cryoconite holes are distinct from the local soils in both 13C and 14C and their isotopic composition is different from similar samples from the Arctic. Carbon contents were generally low (≤0.2%) and older (6–10 ky) than the surrounding soils, suggesting that the cryoconite holes are much more isolated from the atmosphere than the soils.

scholarly journals Eukaryotic Microbial Communities in Japanese Arable Andisols Investigated by Amplicon Sequencing of 18S rRNA Genes

2020 ◽  
Vol 9 (23) ◽  
Author(s):  
Kazumori Mise ◽  
Shigeto Otsuka
Keyword(s):  
Microbial Communities ◽  
18S Rrna ◽  
Amplicon Sequencing ◽  
Rrna Genes ◽  
Community Structures ◽  
Arable Soils ◽  
Eukaryotic Community ◽  
Taxonomic Groups ◽  
18S Rrna Genes

ABSTRACT Compared with the well-studied soil prokaryotic communities, little is known about soil eukaryotic communities. Here, we investigated the eukaryotic community structures in 43 arable soils using amplicon sequencing of 18S rRNA genes. Major taxonomic groups, such as Fungi, Holozoa, and Stramenopiles, were detected in all samples.

scholarly journals Microbial Diversity of Pinnacle and Conical Microbial Mats in the Perennially Ice-Covered Lake Untersee, East Antarctica

2020 ◽  
Vol 11 ◽  
Author(s):  
Carla Greco ◽  
Dale T. Andersen ◽  
Ian Hawes ◽  
Alexander M. C. Bowles ◽  
Marian L. Yallop ◽  
...  
Keyword(s):  
Community Structure ◽  
18S Rrna ◽  
High Throughput Sequencing ◽  
Microbial Mats ◽  
East Antarctica ◽  
Rrna Genes ◽  
Microbial Composition ◽  
Small Spatial Scale ◽  
Lake Floor ◽  
18S Rrna Genes

Antarctic perennially ice-covered lakes provide a stable low-disturbance environment where complex microbially mediated structures can grow. Lake Untersee, an ultra-oligotrophic lake in East Antarctica, has the lake floor covered in benthic microbial mat communities, where laminated organo-sedimentary structures form with three distinct, sympatric morphologies: small, elongated cuspate pinnacles, large complex cones and flat mats. We examined the diversity of prokaryotes and eukaryotes in pinnacles, cones and flat microbial mats using high-throughput sequencing of 16S and 18S rRNA genes and assessed how microbial composition may underpin the formation of these distinct macroscopic mat morphologies under the same environmental conditions. Our analysis identified distinct clustering of microbial communities according to mat morphology. The prokaryotic communities were dominated by Cyanobacteria, Proteobacteria, Verrucomicrobia, Planctomycetes, and Actinobacteria. While filamentous Tychonema cyanobacteria were common in all mat types, Leptolyngbya showed an increased relative abundance in the pinnacle structures only. Our study provides the first report of the eukaryotic community structure of Lake Untersee benthic mats, which was dominated by Ciliophora, Chlorophyta, Fungi, Cercozoa, and Discicristata. The eukaryote richness was lower than for prokaryote assemblages and no distinct clustering was observed between mat morphologies. These findings suggest that cyanobacterial assemblages and potentially other bacteria and eukaryotes may influence structure morphogenesis, allowing distinct structures to form across a small spatial scale.

scholarly journals Effects of Gasterophilus pecorum infestation on the intestinal microbiota of the rewilded Przewalski’s horses in China

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0251512
Author(s):  
Dini Hu ◽  
Yuzhu Chao ◽  
Boru Zhang ◽  
Chen Wang ◽  
Yingjie Qi ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
High Throughput Sequencing ◽  
Nature Reserve ◽  
Sequence Data ◽  
Parasitic Infection ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bioinformatics Analyses ◽  
Gasterophilus Pecorum ◽  
First Time

Horse botflies have been a threat to the Przewalski’s horses in the Kalamaili Nature Reserve in Xinjiang of China since their reintroduction to the original range. As larvae of these parasites could infest the intestine of a horse for months, they could interact with and alter the structure and composition of its intestinal microbiota, affecting adversely its health. Nonetheless, there are no such studies on the rewilded Przewalski’s horses yet. For the first time, this study characterizes the composition of the intestinal microbiota of 7 rewilded Przewalski’s horses infected severely by Gasterophilus pecorum following and prior to their anthelmintic treatment. Bioinformatics analyses of the sequence data obtained by amplicon high throughput sequencing of bacterial 16S rRNA genes showed that G. pecorum infestation significantly increased the richness of the intestinal microbial community but not its diversity. Firmicutes and Bacteroidetes were found the dominant phyla as in other animals, and the parasitic infestation decreased the F/B ratio largely by over 50%. Large reduction in relative abundances of the two genera Streptococcus and Lactobacillus observed with G. pecorum infestation suggested possible changes in colic and digestion related conditions of the infected horses. Variations on the relative abundance of the genus groups known to be pathogenic or symbiotic showed that adverse impact of the G. pecorum infestation could be associated with reduction of the symbiotic genera Lactobacillus and Bifidobacterium that are probiotics and able to promote immunity against parasitic infection.

scholarly journals Humans differ in their personal microbial cloud

PeerJ ◽  
2015 ◽  
Vol 3 ◽  
pp. e1258 ◽  
Author(s):  
James F. Meadow ◽  
Adam E. Altrichter ◽  
Ashley C. Bateman ◽  
Jason Stenson ◽  
GZ Brown ◽  
...  
Keyword(s):  
16S Rrna ◽  
Indoor Air ◽  
Direct Contact ◽  
High Throughput Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Climate Chamber ◽  
Single Person ◽  
First Time

Dispersal of microbes between humans and the built environment can occur through direct contact with surfaces or through airborne release; the latter mechanism remains poorly understood. Humans emit upwards of 106biological particles per hour, and have long been known to transmit pathogens to other individuals and to indoor surfaces. However it has not previously been demonstrated that humans emit a detectible microbial cloud into surrounding indoor air, nor whether such clouds are sufficiently differentiated to allow the identification of individual occupants. We used high-throughput sequencing of 16S rRNA genes to characterize the airborne bacterial contribution of a single person sitting in a sanitized custom experimental climate chamber. We compared that to air sampled in an adjacent, identical, unoccupied chamber, as well as to supply and exhaust air sources. Additionally, we assessed microbial communities in settled particles surrounding each occupant, to investigate the potential long-term fate of airborne microbial emissions. Most occupants could be clearly detected by their airborne bacterial emissions, as well as their contribution to settled particles, within 1.5–4 h. Bacterial clouds from the occupants were statistically distinct, allowing the identification of some individual occupants. Our results confirm that an occupied space is microbially distinct from an unoccupied one, and demonstrate for the first time that individuals release their own personalized microbial cloud.

scholarly journals Diversity, spatial distribution and activity of fungi in freshwater ecosystems

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6247 ◽  
Author(s):  
Cécile Lepère ◽  
Isabelle Domaizon ◽  
Jean-Francois Humbert ◽  
Ludwig Jardillier ◽  
Mylène Hugoni ◽  
...  
Keyword(s):  
18S Rrna ◽  
High Throughput Sequencing ◽  
Taxonomic Composition ◽  
Freshwater Ecosystems ◽  
Rrna Genes ◽  
Active Fraction ◽  
Catchment Areas ◽  
Freshwater Habitats ◽  
Taxonomic Affiliation ◽  
18S Rrna Genes

High-throughput sequencing has given new insights into aquatic fungal community ecology over the last 10 years. Based on 18S ribosomal RNA gene sequences publicly available, we investigated fungal richness and taxonomic composition among 25 lakes and four rivers. We used a single pipeline to process the reads from raw data to the taxonomic affiliation. In addition, we studied, for a subset of lakes, the active fraction of fungi through the 18S rRNA transcripts level. These results revealed a high diversity of fungi that can be captured by 18S rRNA primers. The most OTU-rich groups were Dikarya (47%), represented by putative filamentous fungi more diverse and abundant in freshwater habitats than previous studies have suggested, followed by Cryptomycota (17.6%) and Chytridiomycota (15.4%). The active fraction of the community showed the same dominant groups as those observed at the 18S rRNA genes level. On average 13.25% of the fungal OTUs were active. The small number of OTUs shared among aquatic ecosystems may result from the low abundances of those microorganisms and/or they constitute allochthonous fungi coming from other habitats (e.g., sediment or catchment areas). The richness estimates suggest that fungi have been overlooked and undersampled in freshwater ecosystems, especially rivers, though they play key roles in ecosystem functioning as saprophytes and parasites.

Distinct processes structure bacterioplankton and protist communities across an oceanic front

2020 ◽  
Vol 85 ◽  
pp. 19-34
Author(s):  
R Allen ◽  
TC Summerfield ◽  
K Currie ◽  
PW Dillingham ◽  
LJ Hoffmann
Keyword(s):  
High Throughput Sequencing ◽  
Null Model ◽  
Rrna Genes ◽  
Water Type ◽  
System A ◽  
Deterministic Processes ◽  
Seawater Samples ◽  
18S Rrna Genes ◽  
Abundance And Distribution

Bacterioplankton and protists fulfil key roles in marine ecosystems. Understanding the abundance and distribution of these organisms through space and time is a central focus of biological oceanographers. The role of oceanographic features, in addition to environmental conditions, in structuring bacterioplankton and protist communities has been increasingly recognised. We investigated patterns in bacterioplankton and protist diversity and community structure across the Southland Front system, a compaction of the subtropical front zone, to the east of New Zealand’s South Island. We collected 24 seawater samples across a ~65 km transect and characterised bacterioplankton and protist community composition using high-throughput sequencing of the 16S and 18S rRNA genes, respectively. We identified frontal waters as a bacterioplankton diversity hotspot relative to neighbouring subtropical and subantarctic waters, but did not find evidence of this effect in protists. Bacterioplankton showed pronounced spatial structuring across the front, with communities closely tracking water type through the region. Protist communities also tracked water type through the region, though this effect was substantially less pronounced. We used an ecological null model approach to demonstrate that protist communities are primarily assembled through stochastic processes, whilst bacterioplankton are primarily assembled through deterministic processes across the Southland Front system. We suggest that this divergence emerges from fundamental differences in the characteristics of bacterioplankton and protist communities. Our findings add to a growing body of literature highlighting the importance of oceanographic features in shaping bacterioplankton and protist communities, promoting the necessity for such features to be considered more explicitly in the future.

scholarly journals Structure and diversity of bacterial, eukaryotic and archaeal communities in glacial cryoconite holes from the Arctic and the Antarctic

2012 ◽  
Vol 82 (2) ◽  
pp. 254-267 ◽  
Author(s):  
Karen A. Cameron ◽  
Andrew J. Hodson ◽  
A. Mark Osborn
Keyword(s):  
Rflp Analysis ◽  
The Arctic ◽  
Rrna Genes ◽  
Bacterial Phyla ◽  
Diverse Communities ◽  
Cryoconite Hole ◽  
Life On Earth ◽  
The Antarctic ◽  
First Time ◽  
Archaeal Communities

AbstractThe cryosphere presents some of the most challenging conditions for life on earth. Nevertheless, (micro)biota survive in a range of niches in glacial systems, including water-filled depressions on glacial surfaces termed cryoconite holes (centimetre to metre in diameter and up to 0.5 m deep) that contain dark granular material (cryoconite). In this study, the structure of bacterial and eukaryotic cryoconite communities from ten different locations in the Arctic and Antarctica was compared using T-RFLP analysis of rRNA genes. Community structure varied with geography, with greatest differences seen between communities from the Arctic and the Antarctic. DNA sequencing of rRNA genes revealed considerable diversity, with individual cryoconite hole communities containing between six and eight bacterial phyla and five and eight eukaryotic ‘first-rank’ taxa and including both bacterial and eukaryotic photoautotrophs. Bacterial Firmicutes and Deltaproteobacteria and Epsilonproteobacteria, eukaryotic Rhizaria, Haptophyta, Choanomonada and Centroheliozoa, and archaea were identified for the first time in cryoconite ecosystems. Archaea were only found within Antarctic locations, with the majority of sequences (77%) related to members of the Thaumarchaeota. In conclusion, this research has revealed that Antarctic and Arctic cryoconite holes harbour geographically distinct highly diverse communities and has identified hitherto unknown bacterial, eukaryotic and archaeal taxa, therein.

scholarly journals Occurrence and Genetic Diversity of Babesia caballi and Theileria equi in Chilean Thoroughbred Racing Horses

Pathogens ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 714
Author(s):  
Reinaldo Torres ◽  
Claudio Hurtado ◽  
Sandra Pérez-Macchi ◽  
Pedro Bittencourt ◽  
Carla Freschi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rrna Genes ◽  
Serum Samples ◽  
Theileria Equi ◽  
Babesia Caballi ◽  
Thoroughbred Horses ◽  
18S Rrna Genes ◽  
Thoroughbred Racing ◽  
First Time ◽  
Rhoptry Protein

This study aimed to serologically and molecularly survey Babesia caballi and Theileria equi in thoroughbred horses from racecourses in Chile. Additionally, the genetic diversity of the positive samples was assessed. A total of 286 thoroughbred horses from the Santiago and Valparaíso racecourses had their serum samples submitted to an ELISA for B. caballi and T. equi, and 457 samples (from the Santiago, Valparaíso, and Concepción racecourses) were tested with nested PCRs for the B. caballi 48 KDa rhoptry protein (RAP-1) and T. equi 18S rRNA genes. Selected RAP-1 and 18S positive products were sequenced to perform phylogenetic and haplotype analyses. An overall seroprevalence of 35.6% was observed for these Chilean racecourses: 23.7% for T. equi, 8.4% for B. caballi, and 3.5% for both agents. Overall, a 53.6% occurrence by nPCR was detected for the three Chilean racecourses: 44.2% for T. equi, 5.4% for B. caballi, and 3.9% for both agents. Phylogenetic analysis of T. equi and B. caballi showed genetic proximity with sequences previously detected in other countries. Haplotype analysis revealed a low diversity among the Chilean sequences, which may have originated from those reported in Brazil, Israel, or Cuba. Babesia caballi and T. equi were detected for the first time in Chilean thoroughbred horses.

Description of Rotylenchus arasbaranensis n. sp. from Iran with discussion on the taxonomic status of Plesiorotylenchus Vovlas, Castillo & Lamberti, 1993 (Nematoda: Hoplolaimidae)

Nematology ◽  
2014 ◽  
Vol 16 (9) ◽  
pp. 1019-1045 ◽  
Author(s):  
Mohammad Reza Atighi ◽  
Ebrahim Pourjam ◽  
Razieh Ghaemi ◽  
Majid Pedram ◽  
Gracia Liébanas ◽  
...  
Keyword(s):  
18S Rrna ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Original Description ◽  
Molecular Data ◽  
Rrna Genes ◽  
Molecular Studies ◽  
18S Rrna Genes ◽  
First Time ◽  
Partial 18S

Rotylenchus arasbaranensis n. sp., a new monosexual species is described and illustrated based on morphological, morphometric and molecular studies. The new species is characterised by having an offset and hemispherical lip region with 5-6 annuli, 32-36 μm long stylet, vulva located at 43.9-59.2% with a single epiptygma and rounded tail, rarely bilobed, with 6-8 annuli. The species R. striaticeps and the male of R. buxophilus are reported for the first time from Iran and R. fragaricus is reported and studied for the second time after its original description. The results of the phylogenetic analyses based on the sequences of the D2-D3 expansion region of the 28S, ITS1-rRNA and the partial 18S rRNA genes were provided for the studied species, confirming their differences from each other and determining the position of them and their relationships with closely related taxa. Also, the validity of Plesiorotylenchus is discussed on the basis of molecular data and its synonymisation (with only one sequence) with Rotylenchus is accepted.

A Well-Ordered Thing

2018 ◽  
Author(s):  
Michael D. Gordin
Keyword(s):  
Nineteenth Century ◽  
History Of Science ◽  
Periodic Table ◽  
The Arctic ◽  
Classic Work ◽  
Hot Air ◽  
History Of ◽  
First Time

Dmitrii Mendeleev (1834–1907) is a name we recognize, but perhaps only as the creator of the periodic table of elements. Generally, little else has been known about him. This book is an authoritative biography of Mendeleev that draws a multifaceted portrait of his life for the first time. As the book reveals, Mendeleev was not only a luminary in the history of science, he was also an astonishingly wide-ranging political and cultural figure. From his attack on Spiritualism to his failed voyage to the Arctic and his near-mythical hot-air balloon trip, this is the story of an extraordinary maverick. The ideals that shaped his work outside science also led Mendeleev to order the elements and, eventually, to engineer one of the most fascinating scientific developments of the nineteenth century. This book is a classic work that tells the story of one of the world's most important minds.

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