Image_1_Diversity, distribution, and functional potentials of magroviruses from marine and brackish waters.JPEG

Marine group II (MGII) archaea (Ca. Poseidoniales) are among the most abundant microbes in global oceanic surface waters and play an important role in driving marine biogeochemical cycles. Magroviruses – the viruses of MGII archaea have been recently found to occur ubiquitously in surface ocean. However, their diversity, distribution, and potential ecological functions in coastal zones especially brackish waters are unknown. Here we obtained 234 non-redundant magroviral genomes from brackish surface waters by using homology searches for viral signature proteins highlighting the uncovered vast diversity of this novel viral group. Phylogenetic analysis based on these brackish magroviruses along with previously reported marine ones identified six taxonomic groups with close evolutionary connection to both haloviruses and the viruses of Marine Group I archaea. Magroviruses were present abundantly both in brackish and open ocean samples with some showing habitat specification and others having broad spectrums of distribution between different habitats. Genome annotation suggests they may be involved in regulating multiple metabolic pathways of MGII archaea. Our results uncover the previously overlooked diversity and ecological potentials of a major archaeal virial group in global ocean and brackish waters and shed light on the cryptic evolutionary history of archaeal viruses.</p

Effect of Surface Nanotopography on Immunoaffinity Cell Capture in Microfluidic Devices

Immunoaffinity microfluidic devices have recently become a popular choice to isolate specific cells for many applications. To increase cell capture efficiency, several groups have employed capture beds with nanotopography. However, no systematic study has been performed to quantitatively correlate surface nanopatterns with immunoaffinity cell immobilization. In this work, we controlled substrate topography by depositing close-packed arrays of silica nanobeads with uniform diameters ranging from 100 to 1150 nm onto flat glass. These surfaces were functionalized with a specific antibody and assembled as the base in microfluidic channels, which were then used to capture CD4+ T cells under continuous flow. It is observed that capture efficiency generally increases with nanoparticle size under low flow rate. At higher flow rates, cell capture efficiency becomes increasingly complex; it initially increases with the bead size then gradually decreases. Surprisingly, capture yield plummets atop depositions of some particle diameters. These dips likely stem from dynamic interactions between nanostructures on the substrate and cell membrane as indicated by roughness-insensitive cell capture after glutaraldehyde fixing. This systematic study of surface nanotopography and cell capture efficiency will help optimize the physical properties of microfluidic capture beds for cell isolation from biological fluids

Table_1_Diversity, distribution, and functional potentials of magroviruses from marine and brackish waters.XLSX

Marine group II (MGII) archaea (Ca. Poseidoniales) are among the most abundant microbes in global oceanic surface waters and play an important role in driving marine biogeochemical cycles. Magroviruses – the viruses of MGII archaea have been recently found to occur ubiquitously in surface ocean. However, their diversity, distribution, and potential ecological functions in coastal zones especially brackish waters are unknown. Here we obtained 234 non-redundant magroviral genomes from brackish surface waters by using homology searches for viral signature proteins highlighting the uncovered vast diversity of this novel viral group. Phylogenetic analysis based on these brackish magroviruses along with previously reported marine ones identified six taxonomic groups with close evolutionary connection to both haloviruses and the viruses of Marine Group I archaea. Magroviruses were present abundantly both in brackish and open ocean samples with some showing habitat specification and others having broad spectrums of distribution between different habitats. Genome annotation suggests they may be involved in regulating multiple metabolic pathways of MGII archaea. Our results uncover the previously overlooked diversity and ecological potentials of a major archaeal virial group in global ocean and brackish waters and shed light on the cryptic evolutionary history of archaeal viruses.</p

Data_Sheet_1_Diversity, distribution, and functional potentials of magroviruses from marine and brackish waters.ZIP

Marine group II (MGII) archaea (Ca. Poseidoniales) are among the most abundant microbes in global oceanic surface waters and play an important role in driving marine biogeochemical cycles. Magroviruses – the viruses of MGII archaea have been recently found to occur ubiquitously in surface ocean. However, their diversity, distribution, and potential ecological functions in coastal zones especially brackish waters are unknown. Here we obtained 234 non-redundant magroviral genomes from brackish surface waters by using homology searches for viral signature proteins highlighting the uncovered vast diversity of this novel viral group. Phylogenetic analysis based on these brackish magroviruses along with previously reported marine ones identified six taxonomic groups with close evolutionary connection to both haloviruses and the viruses of Marine Group I archaea. Magroviruses were present abundantly both in brackish and open ocean samples with some showing habitat specification and others having broad spectrums of distribution between different habitats. Genome annotation suggests they may be involved in regulating multiple metabolic pathways of MGII archaea. Our results uncover the previously overlooked diversity and ecological potentials of a major archaeal virial group in global ocean and brackish waters and shed light on the cryptic evolutionary history of archaeal viruses.</p

Data_Sheet_2_Diversity, distribution, and functional potentials of magroviruses from marine and brackish waters.ZIP

Marine group II (MGII) archaea (Ca. Poseidoniales) are among the most abundant microbes in global oceanic surface waters and play an important role in driving marine biogeochemical cycles. Magroviruses – the viruses of MGII archaea have been recently found to occur ubiquitously in surface ocean. However, their diversity, distribution, and potential ecological functions in coastal zones especially brackish waters are unknown. Here we obtained 234 non-redundant magroviral genomes from brackish surface waters by using homology searches for viral signature proteins highlighting the uncovered vast diversity of this novel viral group. Phylogenetic analysis based on these brackish magroviruses along with previously reported marine ones identified six taxonomic groups with close evolutionary connection to both haloviruses and the viruses of Marine Group I archaea. Magroviruses were present abundantly both in brackish and open ocean samples with some showing habitat specification and others having broad spectrums of distribution between different habitats. Genome annotation suggests they may be involved in regulating multiple metabolic pathways of MGII archaea. Our results uncover the previously overlooked diversity and ecological potentials of a major archaeal virial group in global ocean and brackish waters and shed light on the cryptic evolutionary history of archaeal viruses.</p

Effect of Surface Nanotopography on Immunoaffinity Cell Capture in Microfluidic Devices

Immunoaffinity microfluidic devices have recently become a popular choice to isolate specific cells for many applications. To increase cell capture efficiency, several groups have employed capture beds with nanotopography. However, no systematic study has been performed to quantitatively correlate surface nanopatterns with immunoaffinity cell immobilization. In this work, we controlled substrate topography by depositing close-packed arrays of silica nanobeads with uniform diameters ranging from 100 to 1150 nm onto flat glass. These surfaces were functionalized with a specific antibody and assembled as the base in microfluidic channels, which were then used to capture CD4+ T cells under continuous flow. It is observed that capture efficiency generally increases with nanoparticle size under low flow rate. At higher flow rates, cell capture efficiency becomes increasingly complex; it initially increases with the bead size then gradually decreases. Surprisingly, capture yield plummets atop depositions of some particle diameters. These dips likely stem from dynamic interactions between nanostructures on the substrate and cell membrane as indicated by roughness-insensitive cell capture after glutaraldehyde fixing. This systematic study of surface nanotopography and cell capture efficiency will help optimize the physical properties of microfluidic capture beds for cell isolation from biological fluids

Detection of <i>Salmonella</i> spp. Using a Generic and Differential FRET-PCR

<div><p>To facilitate the detection of <i>Salmonella</i> and to be able to rapidly and conveniently determine the species/subspecies present, we developed and tested a generic and differential FRET-PCR targeting their tetrathionate reductase response regulator gene. The differential pan-<i>Salmonella</i> FRET-PCR we developed successfully detected seven plasmids that contained partial sequences of <i>S. bongori</i> and the six <i>S. enterica</i> subspecies. The detection limit varied from ∼5 copies of target gene/per PCR reaction for <i>S. enterica enterica</i> to ∼200 for <i>S. bongori</i>. Melting curve analysis demonstrated a <i>T</i>_m of ∼68°C for <i>S. enterica enterica</i>, ∼62.5°C for <i>S. enterica houtenae</i> and <i>S. enterica diarizonae</i>, ∼57°C for <i>S. enterica indica</i>, and ∼54°C for <i>S. bongori</i>, <i>S. enterica salamae</i> and <i>S. enterica arizonae</i>. The differential pan-<i>Salmonella</i> FRET-PCR also detected and determined the subspecies of 4 reference strains and 47 <i>Salmonella</i> isolated from clinically ill birds or pigs. Finally, we found it could directly detect and differentiate <i>Salmonella</i> in feline (5/50 positive; 10%; one <i>S. enterica salamae</i> and 4 <i>S. enterica enterica</i>) and canine feces (15/114 positive; 13.2%; all <i>S. enterica enterica</i>). The differential pan-<i>Salmonella</i> FRET-PCR failed to react with 96 non-<i>Salmonella</i> bacterial strains. Our experiments show the differential pan-<i>Salmonella</i> FRET-PCR we developed is a rapid, sensitive and specific method to detect and differentiate <i>Salmonella</i>.</p></div

Melting curves of the pan-<i>Salmonella</i> FRET-PCR.

<p>Seven plasmids containing portions of <i>ttrR</i> gene of <i>S. bongori</i> and 6 <i>S. enterica</i> subspecies were used as the positive controls and for melting curve analysis of pan-<i>Salmonella</i> FRET-PCR. The difference in the numbers and types of nucleotide mismatches in the fluorescein and LCRed-640 probes we designed enabled us to identify 4 distinct groups of <i>Salmonella</i> based on their <i>T</i>_m: <i>S. enterica</i> subsp. <i>enterica</i> has a <i>T</i>_m of ∼68°C (pink and solid line); ∼62.5°C for <i>S. enterica</i> subsp. <i>houtenae</i> (blue and solid line) and <i>S. enterica</i> subsp. <i>diarizonae</i> (blue and dashed line); ∼57°C for <i>S. enterica</i> subsp. <i>indica</i> (black and solid line); ∼54°C for <i>S. bongori</i> (green and dashed line), <i>S. enterica</i> subsp. <i>arizonae</i> (red and solid line), and <i>S. enterica</i> subsp. <i>salamae</i> (red and dashed line).</p

Plasmids containing partial <i>Salmonella ttrR</i> gene used in this study.

<p>Plasmids containing partial <i>Salmonella ttrR</i> gene used in this study.</p

<i>Salmonella</i> strains used for selectivity of pan-<i>Salmonella</i> FRET-PCR.

<p><i>Salmonella</i> strains used for selectivity of pan-<i>Salmonella</i> FRET-PCR.</p