Browsing by Author "Karki, Sangita"
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- Comparative Genomics and Environmental Distribution of Large dsDNA Viruses in the Family AsfarviridaeKarki, Sangita; Moniruzzaman, Mohammad; Aylward, Frank O. (2021-03-15)The family Asfarviridae is a group of nucleo-cytoplasmic large DNA viruses (NCLDVs) of which African swine fever virus (ASFV) is well-characterized. Recently the discovery of several Asfarviridae members other than ASFV has suggested that this family represents a diverse and cosmopolitan group of viruses, but the genomics and distribution of this family have not been studied in detail. To this end we analyzed five complete genomes and 35 metagenome-assembled genomes (MAGs) of viruses from this family to shed light on their evolutionary relationships and environmental distribution. The Asfarvirus MAGs derive from diverse marine, freshwater, and terrestrial habitats, underscoring the broad environmental distribution of this family. We present phylogenetic analyses using conserved marker genes and whole-genome comparison of pairwise average amino acid identity (AAI) values, revealing a high level of genomic divergence across disparate Asfarviruses. Further, we found that Asfarviridae genomes encode genes with diverse predicted metabolic roles and detectable sequence homology to proteins in bacteria, archaea, and eukaryotes, highlighting the genomic chimerism that is a salient feature of NCLDV. Our read mapping from Tara oceans metagenomic data also revealed that three Asfarviridae MAGs were present in multiple marine samples, indicating that they are widespread in the ocean. In one of these MAGs we identified four marker genes with > 95% AAI to genes sequenced from a virus that infects the dinoflagellate Heterocapsa circularisquama (HcDNAV). This suggests a potential host for this MAG, which would thereby represent a reference genome of a dinoflagellate-infecting giant virus. Together, these results show that Asfarviridae are ubiquitous, comprise similar sequence divergence as other NCLDV families, and include several members that are widespread in the ocean and potentially infect ecologically important protists.
- Conversion of open pasture to hardwood silvopasture enhanced soil health of an ultisolPoudel, Sanjok; Bansal, Sangeeta; Podder, Swarup; Paneru, Bidur; Karki, Sangita; Fike, John; Kumar, Sandeep (Springer, 2022-12)Black walnut (Juglans nigra) and honeylocust (Gleditsia triacanthos) have gained particular interest for use in silvopastures and other temperate agroforestry systems. However, measures of soil health indicators in these deciduous hardwood silvopastures over time have received limited attention. This study assessed soil health indicators in 25-year-old black walnut- (BSP) and honeylocust-based silvopastures (HSP) and compared with those from adjacent open pasture (OP) systems. Soil samples collected from 0 to 10 cm depth were analyzed for soil organic matter (OM), carbon and nitrogen fractions, glomalin-related soil protein, soil enzymatic activities, and microbial community structure. The soil OM content in HSP (64 g kg(-1)) was greater (p < 0.05) than BSP and OP (55 g kg(-1)). The BSP soils had about 45% and 52% more (p < 0.05) microbial biomass carbon and nitrogen than OP soils. The HSP soils had 60% greater (p < 0.05) microbial biomass nitrogen than OP soils. The BSP supported greater (p < 0.05) beta-glucosidase and urease activities than the HSP and OP treatments, while greater (p < 0.05) beta-glucosidase activity was measured in HSP than OP. Total phospholipid-derived fatty acid and actinomycetes abundance were greater (p < 0.001) in OP compared to BSP and HSP while the arbuscular mycorrhiza fungi abundance was greater (p < 0.05) in OP than in HSP. These findings indicate that black walnut and honeylocust trees in the silvopastures with proper management can improve certain soil health parameters over time depending on tree characteristics and the age of the system.