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

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.

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

Microbiome ◽

10.1186/s40168-021-01156-0 ◽

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.

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Congruency analysis to determine potential surrogates of littoral macroinvertebrate communities: a case study in intertidal ecosystems of northern Yellow Sea

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315412000999 ◽

2012 ◽

Vol 93 (3) ◽

pp. 601-609

Author(s):

Guangjian Xu ◽

Yulian Li ◽

Chongbo He ◽

Henglong Xu

Keyword(s):

Yellow Sea ◽

Northern China ◽

The Yellow Sea ◽

Biological Conservation ◽

Sufficient Information ◽

Macroinvertebrate Communities ◽

Genus Level ◽

Ecological Patterns ◽

Northern Yellow Sea ◽

Mollusc Assemblages

To determine potential surrogates of littoral macroinvertebrate communities for marine bioassessment and for evaluating biological conservation, the different taxonomic resolutions as surrogates were studied based on six datasets collected from intertidal zones of the Yellow Sea, near Qingdao, northern China, during the period of 1989–1998. Samples were collected yearly at five stations with different bottom types during the summer season (June). The genus- and family-level resolutions maintained sufficient information to analyse the ecological patterns of the macroinvertebrate communities for assessing ecological quality status in littoral ecosystems. The mollusc assemblages, alone or in combination with arthropod assemblages, may be used as a surrogate of littoral macroinvertebrate communities, at both species- and genus-level resolutions. The results suggest that the use of simplifications in macroinvertebrate fauna at genus-level resolutions or using smaller taxonomic assemblages (e.g. molluscs and arthropods) are time-efficient and would allow improving sampling strategies of large spatial/temporal scale bioassessment programmes and biological conservation researches in littoral ecosystems.

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

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2021.1756 ◽

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.

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DNase treatment improves viral enrichment in agricultural soil viromes

10.1101/2021.06.01.446688 ◽

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

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

Applied and Environmental Microbiology ◽

10.1128/aem.00531-10 ◽

2010 ◽

Vol 76 (20) ◽

pp. 6724-6732 ◽

Cited By ~ 17

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.

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Trace metals in the waters of the Saguenay fjord

Canadian Journal of Earth Sciences ◽

10.1139/e76-133 ◽

1976 ◽

Vol 13 (9) ◽

pp. 1319-1327 ◽

Cited By ~ 21

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.

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Depletion of coating color components in the blade coating process circulation

TAPPI Journal ◽

10.32964/tj10.9.17 ◽

2011 ◽

Vol 10 (9) ◽

pp. 17-23 ◽

Cited By ~ 1

Author(s):

ANNE RUTANEN ◽

MARTTI TOIVAKKA

Keyword(s):

Fine Particles ◽

Particle Density ◽

Stable Process ◽

Size Fraction ◽

Color Stability ◽

Strong Interactions ◽

Coating Process ◽

Size Segregation ◽

Coating Color ◽

Average Size

Coating color stability, as defined by changes in its solid particle fraction, is important for runnability, quality, and costs of a paper coating operation. This study sought to determine whether the size or density of particles is important in size segregation in a pigment coating process. We used a laboratory coater to study changes in coating color composition during coating operations. The results suggest that size segregation occurs for high and low density particles. Regardless of the particle density, the fine particle size fraction (<0.2 μm) was the most prone for depletion, causing an increase in the average size of the particles. Strong interactions between the fine particles and other components also were associated with a low depletion tendency of fine particles. A stable process and improved efficiency of fine particles and binders can be achieved by controlling the depletion of fine particles.

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Assessment of viral assemblages in different types of wetland water in northeast China using RAPD-PCR

Aquatic Microbial Ecology ◽

10.3354/ame01952 ◽

2020 ◽

Vol 85 ◽

pp. 183-196

Author(s):

Y Sun ◽

J Liu ◽

Q Yao ◽

J Jin ◽

X Liu ◽

...

Keyword(s):

Bacterial Community ◽

Water Samples ◽

Northeast China ◽

Bacterial Community Composition ◽

Freshwater Wetlands ◽

Viral Community ◽

Rapd Pcr ◽

Wetland Water ◽

Different Types ◽

Viral Communities

Viruses are the most abundant and ubiquitous biological entities in various ecosystems, yet few investigations of viral communities in wetlands have been performed. To address this data gap, water samples from 6 wetlands were randomly collected across northeast China; viruses in the water were concentrated by sequential tangential flow filtration, and viral communities were assessed through randomly amplified polymorphic DNA-PCR (RAPD-PCR) with 4 decamer oligonucleotide primers. Principal coordinate analysis and hierarchical clustering analysis of the DNA fingerprints showed that viral community compositions differed among the water samples: communities in the 2 coastal wetlands were more similar to each other than to those in the 4 freshwater wetlands. The Shannon-Weaver index (H) and evenness index (E) of the RAPD-PCR fingerprint also differed among the 6 wetlands. Mantel test revealed that the changes in viral communities in wetland water were most closely related to the water NH4+-N and inorganic C content, followed by total K, P, C and NO3--N. DNA sequence analysis of the excised bands revealed that viruses accounted for ~40% of all sequences. Among the hit viral homologs, the majority belonged to the Microviridae. Moreover, variance partitioning analysis showed that the viral community contributed 24.58% while environmental factors explained 30.56% of the bacterial community variation, indicating that the bacterial community composition was strongly affected by both viral community and water variables. This work provides an initial outline of the viral communities from different types of wetlands in northeast China and improves our understanding of the viral diversity in these ecosystems.

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