scholarly journals Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Anneliek M. ter Horst ◽  
Christian Santos-Medellín ◽  
Jackson W. Sorensen ◽  
Laura A. Zinke ◽  
Rachel M. Wilson ◽  
...  
Keyword(s):  
Protein Content ◽  
Niche Partitioning ◽  
Size Fraction ◽  
Species Boundaries ◽  
Viral Community ◽  
Ecological Patterns ◽  
Significant Enrichment ◽  
Host Ecology ◽  
Depth Water ◽  
Surface Peat

Abstract Background Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland in northern Minnesota (the SPRUCE whole-ecosystem warming experiment and surrounding bog) were analyzed for dsDNA viral community ecological patterns, and the recovered viral populations (vOTUs) were compared with our curated PIGEON database of 266,125 vOTUs from diverse ecosystems. Results Within the SPRUCE experiment, viral community composition was significantly correlated with peat depth, water content, and carbon chemistry, including CH4 and CO2 concentrations, but not with temperature during the first 2 years of warming treatments. Peat vOTUs with aquatic-like signatures (shared predicted protein content with marine and/or freshwater vOTUs) were significantly enriched in more waterlogged surface peat depths. Predicted host ranges for SPRUCE vOTUs were relatively narrow, generally within a single bacterial genus. Of the 4326 SPRUCE vOTUs, 164 were previously detected in other soils, mostly peatlands. None of the previously identified 202,371 marine and freshwater vOTUs in our PIGEON database were detected in SPRUCE peat, but 0.4% of 80,714 viral clusters (VCs, grouped by predicted protein content) were shared between soil and aquatic environments. On a per-sample basis, vOTU recovery was 32 times higher from viromes compared with total metagenomes. Conclusions Results suggest strong viral “species” boundaries between terrestrial and aquatic ecosystems and to some extent between peat and other soils, with differences less pronounced at higher taxonomic levels. The significant enrichment of aquatic-like vOTUs in more waterlogged peat suggests that viruses may also exhibit niche partitioning on more local scales. These patterns are presumably driven in part by host ecology, consistent with the predicted narrow host ranges. Although more samples and increased sequencing depth improved vOTU recovery from total metagenomes, the substantially higher per-sample vOTU recovery after viral particle enrichment highlights the utility of soil viromics.

scholarly journals Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations

2020 ◽  
Author(s):  
Anneliek M ter Horst ◽  
Christian Santos-Medellin ◽  
Jackson W Sorensen ◽  
Laura A Zinke ◽  
Rachel M Wilson ◽  
...  
Keyword(s):  
Niche Partitioning ◽  
Size Fraction ◽  
Species Boundaries ◽  
Genus Level ◽  
Viral Community ◽  
Ecological Patterns ◽  
Significant Enrichment ◽  
Host Ecology ◽  
Depth Water ◽  
Surface Peat

Background: Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland in northern Minnesota (the SPRUCE whole-ecosystem warming experiment and surrounding bog) were analyzed for dsDNA viral community ecological patterns, and the recovered viral populations (vOTUs) were compared to our curated PIGEON database of 266,805 vOTUs from diverse ecosystems. Results: Within the SPRUCE experiment, viral community composition was significantly correlated with peat depth, water content, and carbon chemistry, including CH4 and CO2 concentrations, but not with temperature during the first two years of warming treatments. Peat vOTUs with aquatic-like signatures (shared predicted protein content with marine and/or freshwater vOTUs) were significantly enriched in more waterlogged surface peat depths. Predicted host ranges for SPRUCE vOTUs were relatively narrow, generally within a single bacterial genus. Of the 4,326 SPRUCE vOTUs, 164 were previously detected in other soils, mostly peatlands. None of the previously identified 202,372 marine and freshwater vOTUs in our PIGEON database were detected in SPRUCE peat, but 1.9% of 78,203 genus-level viral clusters (VCs) were shared between soil and aquatic environments. On a per-sample basis, vOTU recovery was 32 times higher from viromes compared to total metagenomes. Conclusions: Results suggest strong viral "species" boundaries between terrestrial and aquatic ecosystems and to some extent between peat and other soils, with differences less pronounced at the "genus" level. The significant enrichment of aquatic-like vOTUs in more waterlogged peat suggests that viruses may also exhibit niche partitioning on more local scales. These patterns are presumably driven in part by host ecology, consistent with the predicted narrow host ranges. Although more samples and increased sequencing depth improved vOTU recovery from total metagenomes, the substantially higher per-sample vOTU recovery after viral particle enrichment highlights the utility of soil viromics.

Mitonuclear interactions and introgression genomics of macaque monkeys ( Macaca ) highlight the influence of behaviour on genome evolution

2021 ◽  
Vol 288 (1960) ◽  
Author(s):  
Ben J. Evans ◽  
Benjamin M. Peter ◽  
Don J. Melnick ◽  
Noviar Andayani ◽  
Jatna Supriatna ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Indirect Effects ◽  
Genomic Data ◽  
Species Boundaries ◽  
Mitochondrial Genomes ◽  
Runs Of Homozygosity ◽  
Interaction Partners ◽  
Significant Enrichment ◽  
Compensatory Mutations ◽  
Multiple Species

In most macaques, females are philopatric and males migrate from their natal ranges, which results in pronounced divergence of mitochondrial genomes within and among species. We therefore predicted that some nuclear genes would have to acquire compensatory mutations to preserve compatibility with diverged interaction partners from the mitochondria. We additionally expected that these sex-differences would have distinctive effects on gene flow in the X and autosomes. Using new genomic data from 29 individuals from eight species of Southeast Asian macaque, we identified evidence of natural selection associated with mitonuclear interactions, including extreme outliers of interspecies differentiation and metrics of positive selection, low intraspecies polymorphism and atypically long runs of homozygosity associated with nuclear-encoded genes that interact with mitochondria-encoded genes. In one individual with introgressed mitochondria, we detected a small but significant enrichment of autosomal introgression blocks from the source species of her mitochondria that contained genes which interact with mitochondria-encoded loci. Our analyses also demonstrate that sex-specific demography sculpts genetic exchange across multiple species boundaries. These findings show that behaviour can have profound but indirect effects on genome evolution by influencing how interacting components of different genomic compartments (mitochondria, the autosomes and the sex chromosomes) move through time and space.

scholarly journals DNase treatment improves viral enrichment in agricultural soil viromes

2021 ◽  
Author(s):  
Jackson W Sorensen ◽  
Joanne B. Emerson ◽  
Laura A Zinke ◽  
Anneliek M ter Horst ◽  
Christian Santos-Medellín ◽  
...  
Keyword(s):  
Size Fraction ◽  
Frozen Storage ◽  
Viral Diversity ◽  
Viral Dna ◽  
Read Mapping ◽  
Resultant Data ◽  
Dnase Treatment ◽  
Ecological Patterns ◽  
Viral Communities ◽  
Microbial Dna

The small genomes of most viruses make it difficult to fully capture viral diversity in metagenomes dominated by DNA from cellular organisms. Viral size-fraction metagenomics (viromics) protocols facilitate enrichment of viral DNA from environmental samples, and these protocols typically include a DNase treatment of the post-0.2 μm viromic fraction to remove contaminating free DNA prior to virion lysis. However, DNase may also remove desirable viral genomic DNA (e.g., contained in virions compromised due to frozen storage or laboratory processing), suggesting that DNase-untreated viromes might be useful in some cases. In order to understand how virome preparation with and without DNase treatment influences the resultant data, here we compared 15 soil viromes (7 DNase-treated, 8 untreated) from 8 samples collected from agricultural fields prior to tomato planting. DNase-treated viromes yielded significantly more assembled viral contigs, contained significantly less non-viral microbial DNA, and recovered more viral populations (vOTUs) through read mapping. However, DNase-treated and untreated viromes were statistically indistinguishable, in terms of ecological patterns across viral communities. Although results suggest that DNase treatment is preferable where possible, in comparison to previously reported total metagenomes from the same samples, both DNase-treated and untreated viromes were significantly enriched in viral signatures by all metrics compared, including a ~225 times greater proportion of viral reads in untreated viromes compared to total metagenomes. Thus, even without DNase treatment, viromics was preferable to total metagenomics for capturing viral diversity in these soils, suggesting that preparation of DNase-untreated viromes can be worthwhile when DNase treatment is not possible

scholarly journals Randomly Amplified Polymorphic DNA Reveals Tight Links between Viruses and Microbes in the Bathypelagic Zone of the Northwestern Mediterranean Sea

2010 ◽  
Vol 76 (20) ◽  
pp. 6724-6732 ◽  
Author(s):  
Christian Winter ◽  
Markus G. Weinbauer
Keyword(s):  
Mediterranean Sea ◽  
In Silico ◽  
Temporal Dynamics ◽  
Size Fraction ◽  
Pcr Analysis ◽  
Randomly Amplified Polymorphic Dna ◽  
Viral Origin ◽  
Viral Community ◽  
Rapd Pcr ◽  
Bathypelagic Zone

ABSTRACT The study site located in the Mediterranean Sea was visited eight times in 2005 and 2006 to collect samples from the epipelagic (5 m), mesopelagic (200 m, 600 m), and bathypelagic (1,000 m, 2,000 m) zones. Randomly amplified polymorphic DNA PCR (RAPD-PCR) analysis was used to obtain fingerprints from microbial and viral size fractions using two different primers each. Depending on the primer used, the number of bands in the water column varied between 12 to 24 and 6 to 19 for the microbial size fraction and between 16 to 26 and 8 to 22 for the viral size fraction. The majority of sequences from the microbial fraction was related to Alphaproteobacteria, Cyanobacteria, Gammaproteobacteria, Firmicutes, and Eukaryota. Only 9% of sequences obtained from the viral fraction were of identifiable viral origin; however, 76% of sequences had no close relatives in the nr database of GenBank. Only 20.1% of complete phage genomes tested in silico resulted in potential RAPD-PCR products, and only 12% of these were targeted by both primers. Also, in silico analysis indicated that RAPD-PCR profiles obtained by the two different primers are largely representative of two different subsets of the viral community. Also, correlation analyses and Mantel tests indicate that the links between changes in the microbial and viral community were strongest in the bathypelagic. Thus, these results suggest a strong codevelopment of virus and host communities in deep waters. The data also indicate that virus communities in the bathypelagic zone can exhibit substantial temporal dynamics.

Trace metals in the waters of the Saguenay fjord

1976 ◽  
Vol 13 (9) ◽  
pp. 1319-1327 ◽  
Author(s):  
P. A. Yeats ◽  
J. M. Bewers
Keyword(s):  
Trace Metals ◽  
Western Basin ◽  
Dissolved Iron ◽  
Copper Nickel ◽  
Saguenay Fjord ◽  
Suspended Particulate ◽  
Spring Freshet ◽  
Significant Enrichment ◽  
Iron Iron ◽  
Depth Water

The distributions of the trace metals iron, zinc, copper, nickel, cobalt, and cadmium in the Saguenay fjord have been determined during the spring freshet. Whereas the mean concentrations of copper, nickel, and zinc are only slightly higher than those in the northwest Atlantic Ocean, the levels of cadmium and cobalt are about three to six times higher, and iron up to two orders of magnitude higher, than ocean water. The significant enrichment of all these metals, with the exceptions of zinc and cadmium, in the surface water relative to the intermediate depth water reflects runoff inputs. The concentrations of total and dissolved iron decrease with increasing salinity, but the nonlinearity of the relationships between the metal concentrations and salinity indicates that significant quantities of iron are lost from the water column in the fjord. Except near the head of the fjord, where flocculation and sedimentation processes appear to be removing large quantities of river-borne iron, iron comprises a constant 11% of the suspended particulate matter. The residence time and budget for iron in the larger western basin of the fjord indicate that 47% of the iron that enters the basin is rapidly removed to the underlying sediments.

Protein content of 5 algae from Persian gulf and Arabian sea

Planta Medica ◽  
2010 ◽  
Vol 76 (12) ◽  
Author(s):  
N Ebrahimi ◽  
M Moein ◽  
S Moein
Keyword(s):  
Protein Content ◽  
Persian Gulf ◽  
Arabian Sea

Manipulation of NOS activity in the context of glucose stress alters AMPK and mitochondrial oxphos protein content

Planta Medica ◽  
2016 ◽  
Vol 81 (S 01) ◽  
pp. S1-S381
Author(s):  
AC Keller ◽  
LA Knaub ◽  
PM McClatchey ◽  
CA Connon ◽  
JEB Reusch
Keyword(s):  
Protein Content

Comparative Study of Size, Total Protein, Fibrinogen and 5-HT Content of Human and Canine Platelet Density Subpopulations

1986 ◽  
Vol 56 (03) ◽  
pp. 288-292 ◽  
Author(s):  
Diego Mezzano ◽  
Eduardo Aranda ◽  
Arnaldo Foradori
Keyword(s):  
Comparative Study ◽  
Protein Content ◽  
Cell Density ◽  
Total Protein ◽  
Unit Volume ◽  
Low Density ◽  
Dense Bodies ◽  
Artifactual Changes ◽  
Platelet Release ◽  
The Difference

SummaryThe size, total protein, fibrinogen and 5-HT content were evaluated in density subpopulations of human and canine platelets fractionated in linear arabinogalactan gradients. The methodology was assessed to ascertain that platelet separation was by density and to discard artifactual changes and platelet release during the procedure. EDTA or PGEi increased the size of human PRP-platelets, but not of dog platelets. In humans, high density (HD) platelets were 1.26 times larger and contained 1.88 times more fibrinogen, 2.23 times more 5-HT and 1.37 times more protein than low density (LD) platelets; in dogs, these density cohorts did not differ in protein content, but LD platelets were 1.29 times larger and had 1.33 times more fibrinogen and 5-HT than HD platelets. These findings suggest that cell density is mostly dependent on the protein content per unit volume of platelets (and not on dense bodies). The differences in fibrinogen and 5-HT content between HD and LD cohorts in humans and dogs may be related to platelet age. The difference in volume between HD and LD platelets in dogs is of uncertain interpretation.

ANALISIS FISIKA KIMIA DARI KERANG DARA (Anadara granosa) YANG BERASAL DARI KAYUTANYO KAB. BANGGAI The Analysis of physical chemical from dara shells (Anadara granosa) origin from Kayutanyo, Kab.Banggai

2018 ◽  
Vol 2 (2) ◽  
Author(s):  
SULASMI ANGGO
Keyword(s):  
Protein Content ◽  
Water Content ◽  
Water Solubility ◽  
Gravimetric Method ◽  
Fat Content ◽  
Carbohydrate Content ◽  
Dust Content ◽  
Total Dust ◽  
Physical Chemical ◽  
Anadara Granosa

The Analysis of physical chemical from dara shells (Anadara granosa) origin from Kayutanyo, kab. Banggai, has been conducted.Dara shell meat is sleaned and dried and after that powered with blender. Determine % rendement, water bonding capacity and index water solubility with Anderson method, coarse fat content with gravimetric method and carbohydrate method with “bye difference” decrease method.The result of analysis showed rendement value is 24,35%, water bonding capacity is 1,6248 gram/ml, index water solubility is 0,202 gram/ml, water content is 79,0045%, total dust content is 1,072%, coarse protein content is 2,25%, coarse fat content is 8,47%, carbohydrate content is 9,2035%. Keyword : Dara shells, (Anadara granosa), analysis physical chemical

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