High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems

CRISPR-Cas are adaptive immune systems that protect their hosts against viruses and other parasitic mobile genetic elements. Consequently, selection from viruses and other genetic parasites is often assumed to drive the acquisition and maintenance of these immune systems in nature, but this remains untested. Here, we analyse the abundance of CRISPR arrays in natural environments using metagenomic datasets from 332 terrestrial, aquatic and host-associated ecosystems. For each metagenome we quantified viral abundance and levels of viral community diversity to test whether these variables can explain variation in CRISPR-Cas abundance across ecosystems. We find a strong positive correlation between CRISPR-Cas abundance and viral abundance. In addition, when controlling for differences in viral abundance, we found that the CRISPR-Cas systems are more abundant when viral diversity is low. We also found differences in relative CRISPR-Cas abundance among environments, with environmental classification explaining ~24% of variation in CRISPR-Cas abundance. However, the correlations with viral abundance and diversity are broadly consistent across diverse natural environments. These results indicate that viral abundance and diversity are major ecological factors that drive the selection and maintenance of CRISPR-Cas in microbial ecosystems.

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Insights into Microbe-Microbe Interactions in Human Microbial Ecosystems: Strategies to be Competitive

10.3389/978-2-88945-052-7 ◽

2016 ◽

Keyword(s):

Microbial Ecosystems ◽

Microbe Interactions

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Recent Rapid Climate Changes in Antarctic and their Influence on Low Diversity Ecosystems

Papers on Global Change IGBP ◽

10.2478/v10190-010-0002-6 ◽

2010 ◽

Vol 17 (1) ◽

pp. 17-30 ◽

Cited By ~ 1

Author(s):

Katarzyna J. Chwedorzewska

Keyword(s):

Environmental Variables ◽

Climate Changes ◽

Biological Significance ◽

Global Changes ◽

Factors Affecting ◽

Low Diversity ◽

Main Factors ◽

The Antarctic ◽

High Diversity ◽

Temperature Water

ABSTRACTThe geographic position, astronomic factors (e.g. the Earth’s maximum distance from the Sun during winter), ice cover and altitude are the main factors affecting the climate of the Antarctic, which is the coldest place on Earth. Parts of Antarctica are facing the most rapid rates of anthropogenic climate change currently seen on the planet. Climate changes are occurring throughout Antarctica, affecting three major groups of environmental variables of considerable biological significance: temperature, water, UV-B radiation.Low diversity ecosystems are expected to be more vulnerable to global changes than high diversity ecosystems

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Lithostratigraphy of the Kweekvlei Formation (Witteberg Group), Cape Supergroup

South African Journal of Geology ◽

10.25131/gssajg.120.3.421 ◽

2017 ◽

Vol 120 (3) ◽

pp. 421-432 ◽

Cited By ~ 2

Author(s):

C. Browning ◽

M. Reid

Keyword(s):

South Africa ◽

Transition Zone ◽

Distal Part ◽

Vascular Plant ◽

Trace Fossil ◽

Plant Debris ◽

Lower Carboniferous ◽

Fossil Assemblage ◽

Low Diversity ◽

Storm Wave

AbstractThe Lower Carboniferous, probably Tournaisian, Kweekvlei Formation is part of the Witteberg Group (Cape Supergroup) of South Africa. Together with the overlying Floriskraal Formation, it forms an upward-coarsening succession within the Lake Mentz Subgroup. Sedimentary features of the Kweekvlei Formation suggest deposition in a storm-wave dominated marine setting, within the storm-influenced, distal part of an offshore transition zone environment. This predominantly argillaceous formation preserves a low diversity trace fossil assemblage. Reworked vascular plant debris (including the problematic genus Praeramunculus sp.) and a shark spine have been reported for the Kweekvlei Formation. There are no known stratigraphic equivalents in South Africa.

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HIGH ABUNDANCE AND LOW DIVERSITY OF TETRAPOD VERTEBRATES IN THE SOLITE QUARRY LAGERSTÄTTE (UPPER TRIASSIC, VIRGINIA-NORTH CAROLINA)

10.1130/abs/2016se-273827 ◽

2016 ◽

Author(s):

Alexander K. Hastings ◽

◽

Christina J. Byrd

Keyword(s):

North Carolina ◽

Upper Triassic ◽

High Abundance ◽

Low Diversity

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Genomic Characterization of the Three Balkan Livestock Guardian Dogs

Sustainability ◽

10.3390/su13042289 ◽

2021 ◽

Vol 13 (4) ◽

pp. 2289

Author(s):

Mateja Janeš ◽

Minja Zorc ◽

Maja Ferenčaković ◽

Ino Curik ◽

Peter Dovč ◽

...

Keyword(s):

Conservation Management ◽

Diversity Management ◽

Genomic Diversity ◽

Mountainous Areas ◽

Autosomal Snps ◽

The Balkans ◽

Gray Wolves ◽

Low Diversity ◽

Genomic Characterization

Balkan Livestock Guardian Dogs (LGD) were bred to help protect sheep flocks in sparsely populated, remote mountainous areas in the Balkans. The aim of this study was genomic characterization (107,403 autosomal SNPs) of the three LGD breeds from the Balkans (Karst Shepherd, Sharplanina Dog, and Tornjak). Our analyses were performed on 44 dogs representing three Balkan LGD breeds, as well as on 79 publicly available genotypes representing eight other LGD breeds, 70 individuals representing seven popular breeds, and 18 gray wolves. The results of multivariate, phylogenetic, clustering (STRUCTURE), and FST differentiation analyses showed that the three Balkan LGD breeds are genetically distinct populations. While the Sharplanina Dog and Tornjak are closely related to other LGD breeds, the Karst Shepherd is a slightly genetically distinct population with estimated influence from German Shepard (Treemix analysis). Estimated genomic diversity was high with low inbreeding in Sharplanina Dog (Ho = 0.315, He = 0.315, and FROH>2Mb = 0.020) and Tornjak (Ho = 0.301, He = 0.301, and FROH>2Mb = 0.033) breeds. Low diversity and high inbreeding were estimated in Karst Shepherds (Ho = 0.241, He = 0.222, and FROH>2Mb = 0.087), indicating the need for proper diversity management. The obtained results will help in the conservation management of Balkan LGD dogs as an essential part of the specific grazing biocultural system and its sustainable maintenance.

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CaptureSeq: Hybridization-Based Enrichment of cpn60 Gene Fragments Reveals the Community Structures of Synthetic and Natural Microbial Ecosystems

Microorganisms ◽

10.3390/microorganisms9040816 ◽

2021 ◽

Vol 9 (4) ◽

pp. 816

Author(s):

Matthew G. Links ◽

Tim J. Dumonceaux ◽

E. Luke McCarthy ◽

Sean M. Hemmingsen ◽

Edward Topp ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Dna Sequences ◽

Pcr Amplification ◽

Shotgun Sequencing ◽

Natural Ecosystems ◽

Gene Markers ◽

Microbial Profile ◽

Microbial Ecosystems ◽

Pcr Targeting

Background. The molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with “universal” PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics. Methods. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir. Results. The CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health. Conclusions: cpn60-based hybridization enriched for taxonomically informative DNA sequences from complex mixtures. In synthetic and natural microbial ecosystems, CaptureSeq provided sequences from prokaryotes and eukaryotes simultaneously, with quantitatively reliable read abundances. CaptureSeq provides an alternative to PCR amplification of taxonomic markers with deep community coverage while minimizing amplification biases.

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Biopolymeric Materials Used as Nonviral Vectors: A Review

Polysaccharides ◽

10.3390/polysaccharides2010007 ◽

2021 ◽

Vol 2 (1) ◽

pp. 100-109

Author(s):

Jailson de Araújo Santos ◽

Daniel Barbosa Liarte ◽

Alessandra Braga Ribeiro ◽

Marcia dos Santos Rizzo ◽

Marcília Pinheiro da Costa ◽

...

Keyword(s):

Chemical Structure ◽

Web Of Science ◽

Gene Transfection ◽

Genetic Material ◽

Nonviral Vectors ◽

Cationic Polymers ◽

Genetic Trait ◽

Low Diversity ◽

Different Types ◽

Materials Used

Bacterial transformation and gene transfection can be understood as being the results of introducing specific genetic material into cells, resulting in gene expression, and adding a new genetic trait to the host cell. Many studies have been carried out to investigate different types of lipids and cationic polymers as promising nonviral vectors for DNA transfer. The present study aimed to carry out a systematic review on the use of biopolymeric materials as nonviral vectors. The methodology was carried out based on searches of scientific articles and applications for patents published or deposited from 2006 to 2020 in different databases for patents (EPO, USPTO, and INPI) and articles (Scopus, Web of Science, and Scielo). The results showed that there are some deposits of patents regarding the use of chitosan as a gene carrier. The 16 analyzed articles allowed us to infer that the use of biopolymers as nonviral vectors is limited due to the low diversity of biopolymers used for these purposes. It was also observed that the use of different materials as nonviral vectors is based on chemical structure modifications of the material, mainly by the addition of cationic groups. Thus, the use of biopolymers as nonviral vectors is still limited to only a few polysaccharide types, emphasizing the need for further studies involving the use of different biopolymers in processes of gene transfer.

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