scholarly journals Increases in the abundance of microbial genes encoding halotolerance and photosynthesis along a sediment salinity gradient

2012 ◽  
Vol 9 (2) ◽  
pp. 815-825 ◽  
Author(s):  
T. C. Jeffries ◽  
J. R. Seymour ◽  
K. Newton ◽  
R. J. Smith ◽  
L. Seuront ◽  
...  
Keyword(s):  
Microbial Community ◽  
Dna Sequences ◽  
Salinity Gradient ◽  
Compatible Solutes ◽  
Environmental Parameters ◽  
Sediment Samples ◽  
Genetic Potential ◽  
Genes Encoding ◽  
Physical And Chemical ◽  
Photosynthesis Gene

Abstract. Biogeochemical cycles are driven by the metabolic activity of microbial communities, yet the environmental parameters that underpin shifts in the functional potential coded within microbial community genomes are still poorly understood. Salinity is one of the primary determinants of microbial community structure and can vary strongly along gradients within a variety of habitats. To test the hypothesis that shifts in salinity will also alter the bulk biogeochemical potential of aquatic microbial assemblages, we generated four metagenomic DNA sequence libraries from sediment samples taken along a continuous, natural salinity gradient in the Coorong lagoon, Australia, and compared them to physical and chemical parameters. A total of 392483 DNA sequences obtained from four sediment samples were generated and used to compare genomic characteristics along the gradient. The most significant shifts along the salinity gradient were in the genetic potential for halotolerance and photosynthesis, which were more highly represented in hypersaline samples. At these sites, halotolerance was achieved by an increase in genes responsible for the acquisition of compatible solutes – organic chemicals which influence the carbon, nitrogen and methane cycles of sediment. Photosynthesis gene increases were coupled to an increase in genes matching Cyanobacteria, which are responsible for mediating CO2 and nitrogen cycles. These salinity driven shifts in gene abundance will influence nutrient cycles along the gradient, controlling the ecology and biogeochemistry of the entire ecosystem.

scholarly journals Increases in the abundance of microbial genes encoding halotolerance and photosynthesis along a sediment salinity gradient

2011 ◽  
Vol 8 (4) ◽  
pp. 7551-7574 ◽  
Author(s):  
T. C. Jeffries ◽  
J. R. Seymour ◽  
K. Newton ◽  
R. J. Smith ◽  
L. Seuront ◽  
...  
Keyword(s):  
Microbial Community ◽  
Dna Sequences ◽  
Salinity Gradient ◽  
Compatible Solutes ◽  
Environmental Parameters ◽  
Sediment Samples ◽  
Genetic Potential ◽  
Genes Encoding ◽  
Physical And Chemical ◽  
Photosynthesis Gene

Abstract. Biogeochemical cycles are driven by the metabolic activity of microbial communities, yet the environmental parameters that underpin shifts in the functional potential coded within microbial community genomes are still poorly understood. Salinity is one of the primary determinants of microbial community structure and can vary strongly along gradients within a variety of habitats. To test the hypothesis that shifts in salinity will also alter the bulk biogeochemical potential of aquatic microbial assemblages, we generated four metagenomic DNA sequence libraries from sediment samples taken along a continuous, natural salinity gradient in the Coorong lagoon, Australia, and compared them to physical and chemical parameters. A total of 392483 DNA sequences obtained from four sediment samples were generated and used to compare genomic characteristics along the gradient. The most significant shifts along the salinity gradient were in the genetic potential for halotolerance and photosynthesis, which were more highly represented in hypersaline samples. At these sites, halotolerance was achieved by an increase in genes responsible for the acquisition of compatible solutes – organic chemicals which influence the carbon, nitrogen and methane cycles of sediment. Photosynthesis gene increases were coupled to an increase in genes matching Cyanobacteria, which are responsible for mediating CO2 and nitrogen cycles. These salinity driven shifts in gene abundance will influence nutrient cycles along the gradient, controlling the ecology and biogeochemistry of the entire ecosystem.

scholarly journals Investigation of the suitability of Remane’s “species minimum” concept in a Mediterranean transitional waters ecosystem

2015 ◽  
Author(s):  
Christina Pavloudi ◽  
Anastasis Oulas ◽  
Jon B Kristoffersen ◽  
Michael W Friedrich ◽  
Christos Arvanitidis
Keyword(s):  
Salinity Gradient ◽  
Environmental Parameters ◽  
Taxonomic Diversity ◽  
Rrna Gene ◽  
Sediment Samples ◽  
Open Sea ◽  
The Baltic ◽  
Water Ecosystems ◽  
Shed Light

Remane’s Artenminimum (“species minimum”) concept was developed for the Baltic Sea, the world’s largest semi-enclosed brackish water body with a unique permanent salinity gradient. It argues that taxonomic diversity of macrobenthic organisms is lowest within the horohalinicum, which occurs at salinity 5 to 8, because the number of brackish specialists does not compensate for the decline in marine and freshwater diversity. The aim of the present study was to investigate the sediment bacterial diversity of a transect river-lagoon-open sea, i.e. from freshwater to marine, occurring at Amvrakikos Gulf (Ionian Sea, Western Greece) and to test whether it follows the Remane's concept, both in terms of species composition but also of functionality. DNA was extracted from sediment samples collected in situ from four stations along the aforementioned transect and sequenced for the 16S rRNA gene. In addition, sediment samples were collected for the assessment of benthic macroorganismic diversity. Moreover, several environmental parameters were measured and their correlation with the diversity patterns was explored. The results of the study shed light on the microbial biodiversity of transitional water ecosystems and reveal the effect of salinity on species diversity, both on microorganisms and on macrobenthic organisms.

scholarly journals Investigation of the suitability of Remane’s “species minimum” concept in a Mediterranean transitional waters ecosystem

2015 ◽  
Author(s):  
Christina Pavloudi ◽  
Anastasis Oulas ◽  
Jon B Kristoffersen ◽  
Michael W Friedrich ◽  
Christos Arvanitidis
Keyword(s):  
Salinity Gradient ◽  
Environmental Parameters ◽  
Taxonomic Diversity ◽  
Rrna Gene ◽  
Sediment Samples ◽  
Open Sea ◽  
The Baltic ◽  
Water Ecosystems ◽  
Shed Light

Remane’s Artenminimum (“species minimum”) concept was developed for the Baltic Sea, the world’s largest semi-enclosed brackish water body with a unique permanent salinity gradient. It argues that taxonomic diversity of macrobenthic organisms is lowest within the horohalinicum, which occurs at salinity 5 to 8, because the number of brackish specialists does not compensate for the decline in marine and freshwater diversity. The aim of the present study was to investigate the sediment bacterial diversity of a transect river-lagoon-open sea, i.e. from freshwater to marine, occurring at Amvrakikos Gulf (Ionian Sea, Western Greece) and to test whether it follows the Remane's concept, both in terms of species composition but also of functionality. DNA was extracted from sediment samples collected in situ from four stations along the aforementioned transect and sequenced for the 16S rRNA gene. In addition, sediment samples were collected for the assessment of benthic macroorganismic diversity. Moreover, several environmental parameters were measured and their correlation with the diversity patterns was explored. The results of the study shed light on the microbial biodiversity of transitional water ecosystems and reveal the effect of salinity on species diversity, both on microorganisms and on macrobenthic organisms.

DNA methylation in satellite repeats disorders

2019 ◽  
Vol 63 (6) ◽  
pp. 757-771 ◽  
Author(s):  
Claire Francastel ◽  
Frédérique Magdinier
Keyword(s):  
Dna Methylation ◽  
Human Genome ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Satellite Repeats ◽  
Tremendous Progress ◽  
Genes Encoding ◽  
Dna Elements ◽  
Near Future

Abstract Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.

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

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.

scholarly journals Environmental parameters and microbial community profiles as indication towards microbial activities and diversity in aquaponic system compartments

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zala Schmautz ◽  
Carlos A. Espinal ◽  
Andrea M. Bohny ◽  
Fabio Rezzonico ◽  
Ranka Junge ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Profile Analysis ◽  
Operation Mode ◽  
Environmental Parameters ◽  
Plant Production ◽  
Microbial Activities ◽  
Anaerobic Processes ◽  
Abiotic Parameters ◽  
Aerobic And Anaerobic

Abstract Background An aquaponic system couples cultivation of plants and fish in the same aqueous medium. The system consists of interconnected compartments for fish rearing and plant production, as well as for water filtration, with all compartments hosting diverse microbial communities, which interact within the system. Due to the design, function and operation mode of the individual compartments, each of them exhibits unique biotic and abiotic conditions. Elucidating how these conditions shape microbial communities is useful in understanding how these compartments may affect the quality of the water, in which plants and fish are cultured. Results We investigated the possible relationships between microbial communities from biofilms and water quality parameters in different compartments of the aquaponic system. Biofilm samples were analyzed by total community profiling for bacterial and archaeal communities. The results implied that the oxygen levels could largely explain the main differences in abiotic parameters and microbial communities in each compartment of the system. Aerobic system compartments are highly biodiverse and work mostly as a nitrifying biofilter, whereas biofilms in the anaerobic compartments contain a less diverse community. Finally, the part of the system connecting the aerobic and anaerobic processes showed common conditions where both aerobic and anaerobic processes were observed. Conclusion Different predicted microbial activities for each compartment were found to be supported by the abiotic parameters, of which the oxygen saturation, total organic carbon and total nitrogen differentiated clearly between samples from the main aerobic loop and the anaerobic compartments. The latter was also confirmed using microbial community profile analysis.

scholarly journals Origin of Life on Mars: Suitability and Opportunities

Life ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 539
Author(s):  
Benton C. Clark ◽  
Vera M. Kolb ◽  
Andrew Steele ◽  
Christopher H. House ◽  
Nina L. Lanza ◽  
...  
Keyword(s):  
Origin Of Life ◽  
Energy Sources ◽  
Early Earth ◽  
Sediment Samples ◽  
Life On Mars ◽  
Eventual Return ◽  
History Of ◽  
Early Mars ◽  
Chemical Conditions ◽  
Physical And Chemical

Although the habitability of early Mars is now well established, its suitability for conditions favorable to an independent origin of life (OoL) has been less certain. With continued exploration, evidence has mounted for a widespread diversity of physical and chemical conditions on Mars that mimic those variously hypothesized as settings in which life first arose on Earth. Mars has also provided water, energy sources, CHNOPS elements, critical catalytic transition metal elements, as well as B, Mg, Ca, Na and K, all of which are elements associated with life as we know it. With its highly favorable sulfur abundance and land/ocean ratio, early wet Mars remains a prime candidate for its own OoL, in many respects superior to Earth. The relatively well-preserved ancient surface of planet Mars helps inform the range of possible analogous conditions during the now-obliterated history of early Earth. Continued exploration of Mars also contributes to the understanding of the opportunities for settings enabling an OoL on exoplanets. Favoring geochemical sediment samples for eventual return to Earth will enhance assessments of the likelihood of a Martian OoL.

Structural and antigenic polymorphism of the 35- to 48-kilodalton merozoite surface antigen (MSA-2) of the malaria parasite Plasmodium falciparum

1991 ◽  
Vol 11 (2) ◽  
pp. 963-971
Author(s):  
B Fenton ◽  
J T Clark ◽  
C M Khan ◽  
J V Robinson ◽  
D Walliker ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Amino Acid ◽  
Surface Antigen ◽  
Dna Sequences ◽  
Amino Acid Sequences ◽  
Merozoite Surface Antigen ◽  
Parasite Plasmodium ◽  
Genes Encoding ◽  
Parasite Plasmodium Falciparum ◽  
Group B

Merozoite surface antigen MSA-2 of the human parasite Plasmodium falciparum is being considered for the development of a malaria vaccine. The antigen is polymorphic, and specific monoclonal antibodies differentiate five serological variants of MSA-2 among 25 parasite isolates. The variants are grouped into two major serogroups, A and B. Genes encoding two different variants from serogroup A have been sequenced, and their DNA together with deduced amino acid sequences were compared with sequences encoded by other alleles. The comparison shows that the serological classification reflects differences in DNA sequences and deduced primary structure of MSA-2 variants and serogroups. Thus, the overall homologies of DNA and amino acid sequences are over 95% among variants in the same serogroup. In contrast, similarities between the group A variants and a group B variant are only 70 and 64% for DNA and amino acid sequences, respectively. We propose that the MSA-2 protein is encoded by two highly divergent groups of alleles, with limited additional polymorphism displayed within each group.

The Qualitative and Quantitative Distribution of Plankton in the Strait of Georgia in Relation to Certain Oceanographic Factors

1957 ◽  
Vol 14 (4) ◽  
pp. 521-552 ◽  
Author(s):  
Joseph Eugène Henri Légaré
Keyword(s):  
Salinity Gradient ◽  
General Distribution ◽  
Fraser River ◽  
Strait Of Georgia ◽  
Quantitative Distribution ◽  
Qualitative And Quantitative ◽  
Chemical Factors ◽  
Physical And Chemical ◽  
Plankton Communities ◽  
Made In

In order to gain some picture of the seasonal variations in the plankton communities two cruises were made in the Strait of Georgia, one in June 1955, and the other in November 1955; 165 plankton collections were taken, also surface temperatures.The correlation of these data have resulted in a number of conclusions concerning the distribution of plankton in the Strait of Georgia. The chief factor affecting the general distribution of plankton is the salinity gradient. The inflow of fresh water from the Fraser River forms zones of varying properties, and leads to the development of different plankton communities. The extent to which physical and chemical factors may determine the presence or absence of certain organisms from the zones described is discussed.

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