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  1. Xu, Jianping (Ed.)
    ABSTRACT Mitochondria originated from an ancient bacterial endosymbiont that underwent reductive evolution by gene loss and endosymbiont gene transfer to the nuclear genome. The diversity of mitochondrial genomes published to date has revealed that gene loss and transfer processes are ongoing in many lineages. Most well-studied eukaryotic lineages are represented in mitochondrial genome databases, except for the superphylum Retaria—the lineage comprising Foraminifera and Radiolaria. Using single-cell approaches, we determined two complete mitochondrial genomes of Foraminifera and two nearly complete mitochondrial genomes of radiolarians. We report the complete coding content of an additional 14 foram species. We show that foraminiferan and radiolarian mitochondrial genomes contain a nearly fully overlapping but reduced mitochondrial gene complement compared to other sequenced rhizarians. In contrast to animals and fungi, many protists encode a diverse set of proteins on their mitochondrial genomes, including several ribosomal genes; however, some aerobic eukaryotic lineages (euglenids, myzozoans, and chlamydomonas-like algae) have reduced mitochondrial gene content and lack all ribosomal genes. Similar to these reduced outliers, we show that retarian mitochondrial genomes lack ribosomal protein and tRNA genes, contain truncated and divergent small and large rRNA genes, and contain only 14 or 15 protein-coding genes, including nad1 , - 3 ,more »- 4 , - 4L , - 5 , and - 7 , cob , cox1 , - 2 , and - 3 , and atp1 , - 6 , and - 9 , with forams and radiolarians additionally carrying nad2 and nad6 , respectively. In radiolarian mitogenomes, a noncanonical genetic code was identified in which all three stop codons encode amino acids. Collectively, these results add to our understanding of mitochondrial genome evolution and fill in one of the last major gaps in mitochondrial sequence databases. IMPORTANCE We present the reduced mitochondrial genomes of Retaria, the rhizarian lineage comprising the phyla Foraminifera and Radiolaria. By applying single-cell genomic approaches, we found that foraminiferan and radiolarian mitochondrial genomes contain an overlapping but reduced mitochondrial gene complement compared to other sequenced rhizarians. An alternative genetic code was identified in radiolarian mitogenomes in which all three stop codons encode amino acids. Collectively, these results shed light on the divergent nature of the mitochondrial genomes from an ecologically important group, warranting further questions into the biological underpinnings of gene content variability and genetic code variation between mitochondrial genomes.« less
    Free, publicly-accessible full text available April 25, 2024
  2. Free, publicly-accessible full text available June 21, 2023
  3. Structural characterization of the complex [B(β-pinane) 3 ] (1) reveals non-covalent H⋯H contacts that are consistent with the generation of London dispersion energies involving the β-pinane ligand frameworks. The homolytic fragmentations of 1 , and camphane and sabinane analogues ([B(camphane) 3 ] (2) and [B(sabinane) 3 ] (3)) were studied computationally. Isodesmic exchange results showed that London dispersion interactions are highly dependent on the terpene's stereochemistry, with the β-pinane framework providing the greatest dispersion free energy (Δ G = −7.9 kcal mol −1 ) with Grimme's dispersion correction (D3BJ) employed. PMe 3 was used to coordinate to [B(β-pinane) 3 ], giving the complex [Me 3 P–B(β-pinane) 3 ] ( 4 ), which displayed a dynamic coordination equilibrium in solution. The association process was found to be slightly endergonic at 302 K (Δ G = +0.29 kcal mol −1 ).
    Free, publicly-accessible full text available September 1, 2023
  4. Free, publicly-accessible full text available August 1, 2023
  5. Abstract Many challenges remain before we can fully understand the multifaceted role that natural organic matter (NOM) plays in soil and aquatic systems. These challenges remain despite the considerable progress that has been made in understanding NOM’s properties and reactivity using the latest analytical techniques. For nearly 4 decades, the International Humic Substances Society (IHSS, which is a non-profit scientific society) has distributed standard substances that adhere to strict isolation protocols and reference materials that are collected in bulk and originate from clearly defined sites. These NOM standard and reference samples offer relatively uniform materials for designing experiments and developing new analytical methods. The protocols for isolating NOM, and humic and fulvic acid fractions of NOM utilize well-established preparative scale column chromatography and reverse osmosis methods. These standard and reference NOM samples are used by the international scientific community to study NOM across a range of disciplines from engineered to natural systems, thereby seeding the transfer of knowledge across research fields. Recently, powerful new analytical techniques used to characterize NOM have revealed complexities in its composition that transcend the “microbial” vs. “terrestrial” precursor paradigm. To continue to advance NOM research in the Anthropocene epoch, a workshop was convened to identifymore »potential new sites for NOM samples that would encompass a range of sources and precursor materials and would be relevant for studying NOM’s role in mediating environmental and biogeochemical processes. We anticipate that expanding the portfolio of IHSS reference and standard NOM samples available to the research community will enable this diverse group of scientists and engineers to better understand the role that NOM plays globally under the influence of anthropogenic mediated changes.« less
    Free, publicly-accessible full text available January 1, 2024
  6. Redox active species in Arctic lacustrine sediments play an important, regulatory role in the carbon cycle, yet there is little information on their spatial distribution, abundance, and oxidation states. Here, we use voltammetric microelectrodes to quantify the in situ concentrations of redox-active species at high vertical resolution (mm to cm) in the benthic porewaters of an oligotrophic Arctic lake (Toolik Lake, AK, USA). Mn( ii ), Fe( ii ), O 2 , and Fe( iii )-organic complexes were detected as the major redox-active species in these porewaters, indicating both Fe( ii ) oxidation and reductive dissolution of Fe( iii ) and Mn( iv ) minerals. We observed significant spatial heterogeneity in their abundance and distribution as a function of both location within the lake and depth. Microbiological analyses and solid phase Fe( iii ) measurements were performed in one of the Toolik Lake cores to determine the relationship between biogeochemical redox gradients and microbial communities. Our data reveal iron cycling involving both oxidizing (FeOB) and reducing (FeRB) bacteria. Additionally, we profiled a large microbial iron mat in a tundra seep adjacent to an Arctic stream (Oksrukuyik Creek) where we observed Fe( ii ) and soluble Fe( iii ) in amore »highly reducing environment. The variable distribution of redox-active substances at all the sites yields insights into the nature and distribution of the important terminal electron acceptors in both lacustrine and tundra environments capable of exerting significant influences on the carbon cycle.« less