Ancient DNA complements microfossil record in deep-sea subsurface sediments

Deep-sea subsurface sediments are the most important archives of marine biodiversity. Until now, these archives were studied mainly using the microfossil record, disregarding large amounts of DNA accumulated on the deep-sea floor. Accessing ancient DNA (aDNA) molecules preserved down-core would offer unique insights into the history of marine biodiversity, including both fossilized and non-fossilized taxa. Here, we recover aDNA of eukaryotic origin across four cores collected at abyssal depths in the South Atlantic, in up to 32.5 thousand-year-old sediment layers. Our study focuses on Foraminifera and Radiolaria, two major groups of marine microfossils also comprising diverse non-fossilized taxa. We describe their assemblages in down-core sediment layers applying both micropalaeontological and environmental DNA sequencing approaches. Short fragments of the foraminiferal and radiolarian small subunit rRNA gene recovered from sedimentary DNA extracts provide evidence that eukaryotic aDNA is preserved in deep-sea sediments encompassing the last glacial maximum. Most aDNA were assigned to non-fossilized taxa that also dominate in molecular studies of modern environments. Our study reveals the potential of aDNA to better document the evolution of past marine ecosystems and opens new horizons for the development of deep-sea palaeogenomics.

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Fungal Diversity in Deep-Sea Hydrothermal Ecosystems

Applied and Environmental Microbiology ◽

10.1128/aem.00653-09 ◽

2009 ◽

Vol 75 (20) ◽

pp. 6415-6421 ◽

Cited By ~ 211

Author(s):

Thomas Le Calvez ◽

Gaëtan Burgaud ◽

Stéphane Mahé ◽

Georges Barbier ◽

Philippe Vandenkoornhuyse

Keyword(s):

Deep Sea ◽

Fungal Diversity ◽

Terrestrial Ecosystems ◽

Small Subunit ◽

Culture Collection ◽

Point Of View ◽

Rrna Gene ◽

Small Subunit Rrna ◽

Culture Independent ◽

Hydrothermal Ecosystems

ABSTRACT Deep-sea hydrothermal ecosystems are considered oases of life in oceans. Since the discovery of these ecosystems in the late 1970s, many endemic species of Bacteria, Archaea, and other organisms, such as annelids and crabs, have been described. Considerable knowledge has been acquired about the diversity of (micro)organisms in these ecosystems, but the diversity of fungi has not been studied to date. These organisms are considered key organisms in terrestrial ecosystems because of their ecological functions and especially their ability to degrade organic matter. The lack of knowledge about them in the sea reflects the widely held belief that fungi are terrestrial organisms. The first inventory of such organisms in deep-sea hydrothermal environments was obtained in this study. Fungal diversity was investigated by analyzing the small-subunit rRNA gene sequences amplified by culture-independent PCR using DNA extracts from hydrothermal samples and from a culture collection that was established. Our work revealed an unsuspected diversity of species in three of the five fungal phyla. We found a new branch of Chytridiomycota forming an ancient evolutionary lineage. Many of the species identified are unknown, even at higher taxonomic levels in the Chytridiomycota, Ascomycota, and Basidiomycota. This work opens the way to new studies of the diversity, ecology, and physiology of fungi in oceans and might stimulate new prospecting for biomolecules. From an evolutionary point of view, the diversification of fungi in the oceans can no longer be ignored.

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Genetic Diversity of Archaea in Deep-Sea Hydrothermal Vent Environments

Genetics ◽

10.1093/genetics/152.4.1285 ◽

1999 ◽

Vol 152 (4) ◽

pp. 1285-1297 ◽

Cited By ~ 3

Author(s):

Ken Takai ◽

Koki Horikoshi

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Deep Sea ◽

Hydrothermal Vent ◽

Small Subunit ◽

Molecular Phylogenetic Analysis ◽

Rrna Gene ◽

Small Subunit Rrna ◽

Rdna Sequencing ◽

Molecular Phylogenetic

Abstract Molecular phylogenetic analysis of naturally occurring archaeal communities in deep-sea hydrothermal vent environments was carried out by PCR-mediated small subunit rRNA gene (SSU rDNA) sequencing. As determined through partial sequencing of rDNA clones amplified with archaea-specific primers, the archaeal populations in deep-sea hydrothermal vent environments showed a great genetic diversity, and most members of these populations appeared to be uncultivated and unidentified organisms. In the phylogenetic analysis, a number of rDNA sequences obtained from deep-sea hydrothermal vents were placed in deep lineages of the crenarchaeotic phylum prior to the divergence of cultivated thermophilic members of the crenarchaeota or between thermophilic members of the euryarchaeota and members of the methanogen-halophile clade. Whole cell in situ hybridization analysis suggested that some microorganisms of novel phylotypes predicted by molecular phylogenetic analysis were likely present in deep-sea hydrothermal vent environments. These findings expand our view of the genetic diversity of archaea in deep-sea hydrothermal vent environments and of the phylogenetic organization of archaea.

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

Microorganisms ◽

10.3390/microorganisms9010021 ◽

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.

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Differences in Microbial Activity and Microbial Populations of Peat Associated with Suppression of Damping-Off Disease Caused by Pythium sylvaticum

Applied and Environmental Microbiology ◽

10.1128/aem.00313-06 ◽

2006 ◽

Vol 72 (10) ◽

pp. 6452-6460 ◽

Cited By ~ 43

Author(s):

Paul J. Hunter ◽

Geoff M. Petch ◽

Leo A. Calvo-Bado ◽

Tim R. Pettitt ◽

Nick R. Parsons ◽

...

Keyword(s):

Microbial Activity ◽

Denaturing Gradient Gel Electrophoresis ◽

Small Subunit ◽

Disease Suppression ◽

Rrna Gene ◽

Damping Off ◽

Small Subunit Rrna ◽

Pythium Sylvaticum ◽

Gradient Gel Electrophoresis ◽

Microbial Groups

ABSTRACT The microbiological characteristics associated with disease-suppressive peats are unclear. We used a bioassay for Pythium sylvaticum-induced damping-off of cress seedlings to identify conducive and suppressive peats. Microbial activity in unconditioned peats was negatively correlated with the counts of P. sylvaticum at the end of the bioassay. Denaturing gradient gel electrophoresis (DGGE) profiling and clone library analyses of small-subunit rRNA gene sequences from two suppressive and two conducive peats differed in the bacterial profiles generated and the diversity of sequence populations. There were also significant differences between bacterial sequence populations from suppressive and conducive peats. The frequencies of a number of microbial groups, including the Rhizobium-Agrobacterium group (specifically sequences similar to those for the genera Ochrobactrum and Zoogloea) and the Acidobacteria, increased specifically in the suppressive peats, although no single bacterial group was associated with disease suppression. Fungal DGGE profiles varied little over the course of the bioassay; however, two bands associated specifically with suppressive samples were detected. Sequences from these bands corresponded to Basidiomycete yeast genera. Although the DGGE profiles were similar, fungal sequence diversity also increased during the bioassay. Sequences highly similar to those of Cryptococcus increased in relative abundance during the bioassay, particularly in the suppressive samples. This study highlights the importance of using complementary approaches to molecular profiling of complex populations and provides the first report that basidiomycetous yeasts may be associated with the suppression of Pythium-induced diseases in peats.

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Detection of Kobe-typeBabesia microtiassociated with Japanese human babesiosis in field rodents in central Taiwan and southeastern mainland China

Parasitology ◽

10.1017/s0031182008004356 ◽

2008 ◽

Vol 135 (6) ◽

pp. 691-699 ◽

Cited By ~ 12

Author(s):

A. SAITO-ITO ◽

N. TAKADA ◽

F. ISHIGURO ◽

H. FUJITA ◽

Y. YANO ◽

...

Keyword(s):

Mainland China ◽

Small Subunit ◽

Human Infection ◽

Babesia Microti ◽

Rrna Gene ◽

Microscopical Examination ◽

Small Subunit Rrna ◽

Central Taiwan ◽

Field Rodents ◽

Human Babesiosis

SUMMARYField rodent surveys forBabesiainfection were performed from 2002 to 2005 in the vicinities of human babesiosis occurrences in Taiwan and mainland China.Babesia microtiwas identified by microscopical examination and/or PCR in 1Rattus coxingaand 1Crocidura horsfieldiiin central Taiwan and in 13Niviventer confucianusand 1Apodemus agrariusin Zhejiang and Fujian Provinces of southeastern China. Of 15B. microtisamples detected by PCR, all except 1 were shown to be the Kobe-type, the aetiological small subunit rRNA gene-type of the first Japanese patient; the exception was also a Kobe-related type. The Kobe-type had been found in rodents only in a few places including the human infection occurrence place in Japan. The internal transcribed spacer 1 to 2 sequences of the Taiwanese and Chinese Kobe-types were very similar to each other but considerably different (approx. 94% pairwise identities) from that of the Japanese Kobe-type. A Taiwanese Kobe-type strain was serologically differentiated from the Kobe strain originating from the Japanese first patient. The distribution of the Kobe-type in the vicinities of human babesiosis occurrences in Taiwan and China as well as in Japan is suggestive of involvement of the Kobe-type in Asian human babesiosis.

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Phylogenetic analysis of Blastocystis isolates from different hosts based on the comparison of small-subunit rRNA gene sequences

Molecular and Biochemical Parasitology ◽

10.1016/s0166-6851(02)00246-3 ◽

2003 ◽

Vol 126 (1) ◽

pp. 119-123 ◽

Cited By ~ 62

Author(s):

Christophe Noël ◽

Corinne Peyronnet ◽

Delphine Gerbod ◽

Virginia P Edgcomb ◽

Pilar Delgado-Viscogliosi ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Small Subunit ◽

Rrna Gene ◽

Small Subunit Rrna ◽

Gene Sequences ◽

Small Subunit Rrna Gene

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Comparison of bacterial communities in the Solimões and Negro River tributaries of the Amazon River based on small subunit rRNA gene sequences

Genetics and Molecular Research ◽

10.4238/2011.december.8.8 ◽

2011 ◽

Vol 10 (4) ◽

pp. 3783-3793 ◽

Cited By ~ 3

Author(s):

J.C.C. Peixoto ◽

L. Leomil ◽

J.V. Souza ◽

F.B.S. Peixoto ◽

S. Astolfi-Filho

Keyword(s):

Bacterial Communities ◽

Small Subunit ◽

Amazon River ◽

Rrna Gene ◽

Small Subunit Rrna ◽

Gene Sequences ◽

Negro River ◽

Small Subunit Rrna Gene

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Quantitative Measure of Small-Subunit rRNA Gene Sequences of the Kingdom Korarchaeota

Applied and Environmental Microbiology ◽

10.1128/aem.64.12.5064-5066.1998 ◽

1998 ◽

Vol 64 (12) ◽

pp. 5064-5066 ◽

Cited By ~ 21

Author(s):

Clifford F. Brunk ◽

Nicole Eis

Keyword(s):

Internal Standard ◽

Pcr Amplification ◽

Quantitative Measure ◽

Pcr Primers ◽

Small Subunit ◽

Ssu Rdna ◽

Rdna Sequence ◽

Rrna Gene ◽

Small Subunit Rrna ◽

Rdna Sequences

ABSTRACT Comparative PCR amplification of small-subunit (SSU) rRNA gene (rDNA) sequences indicates substantial preferential PCR amplification of pJP27 sequences with korarchaeote-specific PCR primers. The coamplification of a modified SSU rDNA sequence can be used as an internal standard to determine the amount of a specific SSU rDNA sequence.

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