scholarly journals Mapping ecologically important virus-host interactions in geographically diverse solar salterns with metagenomics

2016 ◽  
Author(s):  
Abraham G Moller ◽  
Chun Liang
Keyword(s):  
Microbial Interactions ◽  
High Rate ◽  
Environmental Stability ◽  
Glycerol Metabolism ◽  
Solar Salterns ◽  
Host Interactions ◽  
Taxonomic Profiling ◽  
Nutrient Turnover ◽  
Glycerol 3 Phosphate Dehydrogenase ◽  
Haloquadratum Walsbyi

Solar salterns are excellent model ecosystems for studying virus-microbial interactions because of their low microbial diversity, environmental stability, and high viral density. By using the power of CRISPR spacers to link viruses to their prokaryotic hosts, we explored virus-host interactions in geographically diverse salterns and related them to carbon cycling. Using taxonomic profiling, we identified hosts such as archaeal Haloquadratum, Halorubrum, and Haloarcula and bacterial Salinibacter, and we found that community composition related to not only salinity but also local environmental dynamics. Characterizing glycerol metabolism genes in these metagenomes suggested most dihydroxyacetone kinase genes affiliate to Halorubrum and Haloquadratum while most glycerol-3-phosphate dehydrogenase genes affiliate to Salinibacter. We identified CRISPR spacers in the metagenomes with two different methods and found more spacers in the Halobacteriaceae-dominated IC21 and C34 salterns compared with the Haloquadratum-dominated SS19, SS33, and SS37 salterns, suggesting low CRISPR diversity and possibly a high rate of CRISPR loss in the Haloquadratum-dominated salterns. After CRISPR detection, spacers were aligned against haloviral genomes to map virus to host. While most alignments linked viruses to Haloquadratum walsbyi, there were clusters of interactions with less abundant Haloarcula and Haloferax. Further examination of the dimer and codon usage differences between paired viruses and their hosts and detection of cas genes in the salterns confirmed both the plausibility of virus-host interactions and the possibility of CRISPR activity. Taken together, our studies suggest CRISPR loss in archaeal hosts controls the level of virus proliferation and the nutrient turnover viruses induce in these environments.

scholarly journals Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2844 ◽  
Author(s):  
Abraham G. Moller ◽  
Chun Liang
Keyword(s):  
Microbial Interactions ◽  
Environmental Stability ◽  
Glycerol Metabolism ◽  
Solar Salterns ◽  
Host Interactions ◽  
Taxonomic Profiling ◽  
Dihydroxyacetone Kinase ◽  
Glycerol 3 Phosphate Dehydrogenase ◽  
Haloquadratum Walsbyi ◽  
Metabolism Gene

Solar salterns are excellent model ecosystems for studying virus-microbial interactions because of their low microbial diversity, environmental stability, and high viral density. By using the power of CRISPR spacers to link viruses to their prokaryotic hosts, we explored virus-host interactions in geographically diverse salterns. Using taxonomic profiling, we identified hosts such as archaeal Haloquadratum, Halorubrum, and Haloarcula and bacterial Salinibacter, and we found that community composition related to not only salinity but also local environmental dynamics. Characterizing glycerol metabolism genes in these metagenomes suggested Halorubrum and Haloquadratum possess most dihydroxyacetone kinase genes while Salinibacter possesses most glycerol-3-phosphate dehydrogenase genes. Using two different methods, we detected fewer CRISPR spacers in Haloquadratum-dominated compared with Halobacteriaceae-dominated saltern metagenomes. After CRISPR detection, spacers were aligned against haloviral genomes to map virus to host. While most alignments for each saltern metagenome linked viruses to Haloquadratum walsbyi, there were also alignments indicating interactions with the low abundance taxa Haloarcula and Haloferax. Further examination of the dinucleotide and trinucleotide usage differences between paired viruses and their hosts confirmed viruses and hosts had similar nucleotide usage signatures. Detection of cas genes in the salterns supported the possibility of CRISPR activity. Taken together, our studies suggest similar virus-host interactions exist in different solar salterns and that the glycerol metabolism gene dihydroxyacetone kinase is associated with Haloquadratum and Halorubrum.

scholarly journals Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics

2016 ◽  
Author(s):  
Abraham G Moller ◽  
Chun Liang
Keyword(s):  
Microbial Interactions ◽  
Environmental Stability ◽  
Glycerol Metabolism ◽  
Solar Salterns ◽  
Host Interactions ◽  
Taxonomic Profiling ◽  
Dihydroxyacetone Kinase ◽  
Glycerol 3 Phosphate Dehydrogenase ◽  
Haloquadratum Walsbyi ◽  
Metabolism Gene

Solar salterns are excellent model ecosystems for studying virus-microbial interactions because of their low microbial diversity, environmental stability, and high viral density. By using the power of CRISPR spacers to link viruses to their prokaryotic hosts, we explored virus-host interactions in geographically diverse salterns and related them to carbon cycling. Using taxonomic profiling, we identified hosts such as archaeal Haloquadratum, Halorubrum, and Haloarcula and bacterial Salinibacter, and we found that community composition related to not only salinity but also local environmental dynamics. Characterizing glycerol metabolism genes in these metagenomes suggested Halorubrum and Haloquadratum possess most dihydroxyacetone kinase genes while Salinibacter possesses most glycerol-3-phosphate dehydrogenase genes. We identified CRISPR spacers in the metagenomes with two different methods and found more spacers in the IC21 and C34 salterns compared with the SS19, SS33, and SS37 salterns, suggesting fewer types of CRISPR spacers in the Haloquadratum-majority salterns. After CRISPR detection, spacers were aligned against haloviral genomes to map virus to host. While most alignments linked viruses to Haloquadratum walsbyi, there were groups of interactions with the low abundance taxa Haloarcula and Haloferax. Further examination of the dinucleotide and trinucleotide usage differences between paired viruses and their hosts confirmed viruses and hosts had similar nucleotide usage signatures. Detection of cas genes in the salterns supported the possibility of CRISPR activity. Taken together, our studies suggest similar virus-host interactions exist in different solar salterns and that the glycerol metabolism gene dihydroxyacetone kinase is associated with Haloquadratum and Halorubrum.

scholarly journals Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics

2016 ◽  
Author(s):  
Abraham G Moller ◽  
Chun Liang
Keyword(s):  
Microbial Interactions ◽  
Environmental Stability ◽  
Glycerol Metabolism ◽  
Solar Salterns ◽  
Host Interactions ◽  
Taxonomic Profiling ◽  
Dihydroxyacetone Kinase ◽  
Glycerol 3 Phosphate Dehydrogenase ◽  
Haloquadratum Walsbyi ◽  
Metabolism Gene

Solar salterns are excellent model ecosystems for studying virus-microbial interactions because of their low microbial diversity, environmental stability, and high viral density. By using the power of CRISPR spacers to link viruses to their prokaryotic hosts, we explored virus-host interactions in geographically diverse salterns and related them to carbon cycling. Using taxonomic profiling, we identified hosts such as archaeal Haloquadratum, Halorubrum, and Haloarcula and bacterial Salinibacter, and we found that community composition related to not only salinity but also local environmental dynamics. Characterizing glycerol metabolism genes in these metagenomes suggested Halorubrum and Haloquadratum possess most dihydroxyacetone kinase genes while Salinibacter possesses most glycerol-3-phosphate dehydrogenase genes. We identified CRISPR spacers in the metagenomes with two different methods and found more spacers in the IC21 and C34 salterns compared with the SS19, SS33, and SS37 salterns, suggesting fewer types of CRISPR spacers in the Haloquadratum-majority salterns. After CRISPR detection, spacers were aligned against haloviral genomes to map virus to host. While most alignments linked viruses to Haloquadratum walsbyi, there were groups of interactions with the low abundance taxa Haloarcula and Haloferax. Further examination of the dinucleotide and trinucleotide usage differences between paired viruses and their hosts confirmed viruses and hosts had similar nucleotide usage signatures. Detection of cas genes in the salterns supported the possibility of CRISPR activity. Taken together, our studies suggest similar virus-host interactions exist in different solar salterns and that the glycerol metabolism gene dihydroxyacetone kinase is associated with Haloquadratum and Halorubrum.

scholarly journals Changes of viral and prokaryote abundances in a high rate algal pond using flow cytometry detection

2020 ◽  
Vol 82 (6) ◽  
pp. 1062-1069
Author(s):  
Ashleigh R. Hisee ◽  
Matthew Hisee ◽  
Jody C. McKerral ◽  
Stephanie R. Rosenbauer ◽  
James S. Paterson ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
South Australia ◽  
Rapid Identification ◽  
Microbial Interactions ◽  
High Rate ◽  
Treated Wastewater ◽  
Bacterial Populations ◽  
Flow Cytometry Detection ◽  
Wastewater Samples ◽  
Mixed Systems

Abstract High rate algal ponds (HRAPs) are shallow, mixed systems for wastewater treatment, which use sunlight exposure for disinfection. Little is known regarding the relationships between the bacteria and viruses within HRAP systems. Uniquely, flow cytometry permits the rapid identification of bacterial and viral populations in wastewater samples, separating populations based on genome and particle size. Treated wastewater samples were collected from an HRAP at Kingston on Murray, South Australia. Flow cytometry analysis detected bacterial populations and discriminated virus-like particles (VLP) and large VLP (LVLP). Rapid, short term, fluctuations in the abundance of all three populations were observed. Changes in the abundance of these populations was compared; wastewater composition was used as metadata for the comparisons. Linear regression determined relationships in abundances between bacteria and LVLP (R2 0.2985); LVLP and VLP (R2 0.5829) and bacteria and VLP (R2 0.5778) all with p-values of <0.001. Bacterial, LVLP and VLP abundance positively correlated with each other, indicating potential microbial interactions. Overall, the results suggest a parasitic relationship was occurring and driving the abundances of bacteria and viruses within the system.

scholarly journals Honey as an Ecological Reservoir of Antibacterial Compounds Produced by Antagonistic Microbial Interactions in Plant Nectars, Honey and Honey Bee

Antibiotics ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 551
Author(s):  
Katrina Brudzynski
Keyword(s):  
Antibacterial Activity ◽  
Secondary Metabolites ◽  
Honey Bee ◽  
Biofilm Formation ◽  
Microbial Interactions ◽  
Microbial Colonization ◽  
Antibacterial Compounds ◽  
Fundamental Feature ◽  
Host Interactions ◽  
Cellular Components

The fundamental feature of “active honeys” is the presence and concentration of antibacterial compounds. Currently identified compounds and factors have been described in several review papers without broader interpretation or links to the processes for their formation. In this review, we indicate that the dynamic, antagonistic/competitive microbe–microbe and microbe–host interactions are the main source of antibacterial compounds in honey. The microbial colonization of nectar, bees and honey is at the center of these interactions that in consequence produce a range of defence molecules in each of these niches. The products of the microbial interference and exploitive competitions include antimicrobial peptides, antibiotics, surfactants, inhibitors of biofilm formation and quorum sensing. Their accumulation in honey by horizontal transfer might explain honey broad-spectrum, pleiotropic, antibacterial activity. We conclude that honey is an ecological reservoir of antibacterial compounds produced by antagonistic microbial interactions in plant nectars, honey and honey bee. Thus, refocusing research on secondary metabolites resulting from these microbial interactions might lead to discovery of new antibacterial compounds in honey that are target-specific, i.e., acting on specific cellular components or inhibiting the essential cellular function.

scholarly journals LPL/AQP7/GPD2 promotes glycerol metabolism under hypoxia and prevents cardiac dysfunction during ischemia.

2020 ◽  
Author(s):  
Sohta Ishihama ◽  
Tatsuya Yoshida ◽  
Satoya Yoshida ◽  
Noriyuki Ouchi ◽  
Yu Mori ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Cardiac Dysfunction ◽  
Myocardial Infarct ◽  
Atp Synthesis ◽  
Glycerol Metabolism ◽  
Dihydroxyacetone Phosphate ◽  
Myocardial Infarct Size ◽  
Glucose And Lipid Metabolism ◽  
Acute Mi ◽  
Glycerol 3 Phosphate Dehydrogenase

Abstract Fatty acid constitutes a major energy substrate in the heart to fuel contraction under aerobic conditions. Ischemia downregulates fatty acid metabolism to adapt to the limited oxygen supply and makes glucose the preferred substrate. However, the mechanism of the myocardial metabolic shift during ischemia remains unknown. Here, we show that cardiomyocyte secretion of lipoprotein lipase (LPL), a principal enzyme that converts triglycerides to free fatty acids and glycerol, increased during myocardial infarction (MI). Cardiomyocyte-specific LPL deficiency enhanced cardiac dysfunction and apoptosis following MI. Deficiency of aquaporin 7 (AQP7), a glycerol channel in cardiomyocytes, increased the myocardial infarct size and apoptosis in response to ischemia. Ischemic conditions activated glycerol-3-phosphate dehydrogenase 2 (GPD2), which converts glycerol-3-phosphate into dihydroxyacetone phosphate to facilitate ATP synthesis from glycerol. Conversely, GPD2 deficiency exacerbated cardiac dysfunction after acute MI. Together, these results identify that LPL/AQP7/GPD2-mediated glycerol metabolism plays an important role to bridge glucose and lipid metabolism in MI and prevent myocardial ischemia-related damage.

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