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1. Finding needles in a haystack—Extensive diversity in the eustigmatophyceae revealed by community metabarcode analysis targeting the rbc L gene using lineage‐directed primers

   https://doi.org/10.1111/jpy.13196  

   Fawley, Marvin W. ; Fawley, Karen P. ; Cahoon, Aubrey Bruce ; Lane, ed., C. ( August 2021 , Journal of Phycology)

   Sequences from the Stramenopile class Eustigmatophyceae are rarely reported in metabarcoding studies, and when they have been reported, there are very few haplotypes. We hypothesized that the paucity of eustigmatophyte species detected in these studies may be a result of the metabarcoding techniques used, which have primarily employed universal ribosomal RNA gene regions. In this study, we examined environmental DNA samples from 22 sites in southwestern Virginia, some of which had previously been studied using ribosomal RNA analysis. We used metabarcoding techniques targeting the plastidrbcL gene with new primers designed to produce a 370 bp amplicon from all lineages of the Eustigmatophyceae in a reference collection. The amplicons were then analyzed with DADA2 to produce amplicon sequence variants (ASVs). Our results revealed 184rbcL haplotypes that can be tentatively assigned to the Eustigmatophyceae from these sites, representing much higher diversity than has been detected by ribosomal DNA‐based studies. The techniques employed can be used for future studies of population structure, ecology, distribution, and diversity of this class. With these techniques, it should be possible to make realistic estimates of the species‐level diversity of the Eustigmatophyceae on local, regional, and perhaps global scales.

    

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2. Delocalization-Assisted Transport through Nucleic Acids in Molecular Junctions

   https://doi.org//10.1021/acs.biochem.1c00072  

   Jesús Valdiviezo, Caleb Clever ( April 2021 , Biochemistry)

   null (Ed.)

   The flow of charge through molecules is central to the function of supramolecular machines, and charge transport in nucleic acids is implicated in molecular signaling and DNA repair. We examine the transport of electrons through nucleic acids to understand the interplay of resonant and nonresonant charge carrier transport mechanisms. This study reports STM break junction measurements of peptide nucleic acids (PNAs) with a Gblock structure and contrasts the findings with previous results for DNA duplexes. The conductance of G-block PNA duplexes is much higher than that of the corresponding DNA duplexes of the same sequence; however, they do not display the strong even−odd dependence conductance oscillations found in G-block DNA. Theoretical analysis finds that the conductance oscillation magnitude in PNA is suppressed because of the increased level of electronic coupling interaction between G-blocks in PNA and the stronger PNA−electrode interaction compared to that in DNA duplexes. The strong interactions in the G-block PNA duplexes produce molecular conductances as high as 3% G0, where G0 is the quantum of conductance, for 5 nm duplexes. 

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3. Rapid self‐assembly of γPNA nanofibers at constant temperature

   https://doi.org/10.1002/bip.23463  

   Kumar, Sriram ; Dhami, Isha ; Thadke, Shivaji A. ; Ly, Danith H. ; Taylor, Rebecca E. ( July 2021 , Biopolymers)

   Peptide nucleic acids (PNAs) have primarily been used to achieve therapeutic gene modulation through antisense strategies since their design in the 1990s. However, the application of PNAs as a functional nanomaterial has been more recent. We recently reported thatγ‐modified peptide nucleic acids (γPNAs) could be used to enable formation of complex, self‐assembling nanofibers in select polar aprotic organic solvent mixtures. Here we demonstrate that distinctγPNA strands, each with a high density ofγ‐modifications can form complex nanostructures at constant temperatures within 30 minutes. Additionally, we demonstrate DNA‐assisted isothermal growth ofγPNA nanofibers, thereby overcoming a key hurdle for future scale‐up of applications related to nanofiber growth and micropatterning.

    

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4. The respiratory microbiota of three cohabiting beluga whales (Delphinapterus leucas) under human care

   https://doi.org/10.3389/fmars.2023.1168623  

   Smith, Susan A. ; Ropati, Destiny V. ; Santoferrara, Luciana F. ; Romano, Tracy A. ; McManus, George B. ( December 2023 , Frontiers in Marine Science)

   We sampled the respiratory mucus from voluntary blowhole exhalations (“blow”) of three healthy beluga whales (Delphinapterus leucas) under professional human care. Blow samples were collected from three resident belugas, one adult male (M1) and two adult females (F1, F2), with voluntary behaviors via non-invasive methods over three days in July 2021 (four days for M1). Samples were weighed and examined microscopically for the enumeration of eukaryotic and prokaryotic microbes, and then were used to evaluate carbon substrate use and taxonomic diversity of prokaryotic communities in the host respiratory sytem. Microscopical observations and 18S rRNA gene sequencing indicated the presence of eukaryotic microbiota, the ciliate generaPlanilaminaandKyaroikeusin all three individuals. Exposure of samples to different metabolic carbon substrates indicated significant differences in the number of carbon sources usable by the prokaryotic communities of different whales (range: 11-25 sources), as well as a signficantly decreased diversity of carbon sources used by the community in the habitat water (5 sources). Sequencing of the hypervariable V4 region of the 16S rRNA gene revealed 19 amplicon sequence variants (ASVs) that were present in all whale samples. The oldest femaleD. leucas(F2) had the lowest overall diversity, and was significantly different from M1 and F1 in taxon composition, including an anomalously low ratio of Baccillota: Bacteroidota (0.01) compared to the other whales. In comparisons of microbial community composition, M1 had a significantly higher diversity than F1 and F2. These results suggest that attention should be given to regular microbiome sampling, and indicate a need for the pairing of microbiome and clinical data for animals in aquaria. Overall, these data contribute to the growing database on the core respiratory microbiota in cohabiting cetaceans under professional human care, indicate the utility of non-invasive sampling, and help characterize a baseline for healthyD. leucas.

    

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5. Host genotype controls ecological change in the leaf fungal microbiome

   https://doi.org/10.1371/journal.pbio.3001681  

   VanWallendael, Acer ; Benucci, Gian Maria ; da Costa, Pedro Beschoren ; Fraser, Linnea ; Sreedasyam, Avinash ; Fritschi, Felix ; Juenger, Thomas E. ; Lovell, John T. ; Bonito, Gregory ; Lowry, David B. ( August 2022 , PLOS Biology)

   Dong, Xinnian (Ed.)

   Leaf fungal microbiomes can be fundamental drivers of host plant success, as they contain pathogens that devastate crop plants and taxa that enhance nutrient uptake, discourage herbivory, and antagonize pathogens. We measured leaf fungal diversity with amplicon sequencing across an entire growing season in a diversity panel of switchgrass ( Panicum virgatum ). We also sampled a replicated subset of genotypes across 3 additional sites to compare the importance of time, space, ecology, and genetics. We found a strong successional pattern in the microbiome shaped both by host genetics and environmental factors. Further, we used genome-wide association (GWA) mapping and RNA sequencing to show that 3 cysteine-rich receptor-like kinases (crRLKs) were linked to a genetic locus associated with microbiome structure. We confirmed GWAS results in an independent set of genotypes for both the internal transcribed spacer (ITS) and large subunit (LSU) ribosomal DNA markers. Fungal pathogens were central to microbial covariance networks, and genotypes susceptible to pathogens differed in their expression of the 3 crRLKs, suggesting that host immune genes are a principal means of controlling the entire leaf microbiome. 

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