Unmasking photogranulation in decreasing glacial albedo and net autotrophic wastewater treatment

In both natural and built environments, microbes on occasions manifest in spherical aggregates instead of substratum-affixed biofilms. These microbial aggregates are conventionally referred to as granules. Cryoconites are mineral rich granules that appear on glacier surfaces and are linked with expanding surface darkening, thus decreasing albedo, and enhanced melt. The oxygenic photogranules (OPGs) are organic rich granules that grow in wastewater, which enables wastewater treatment with photosynthetically produced oxygen and which presents potential for net autotrophic wastewater treatment in a compact system. Despite obvious differences inherent in the two, cryoconite and OPG pose striking resemblance. In both, the order Oscillatoriales in Cyanobacteria envelope inner materials and develop dense spheroidal aggregates. We explore the mechanism of photogranulation on account of high similarity between cryoconites and OPGs. We contend that there is no universal external cause for photogranulation. However, cryoconites and OPGs, as well as their intravariations, which are all under different stress fields, are the outcome of universal physiological processes of the Oscillatoriales interfacing with goldilocks interactions of stresses. Finding the rules of photogranulation may enhance engineering of glacier and wastewater systems to manipulate their ecosystem impacts.     

MassBase: A large-scaled depository of mass spectrometry datasets for metabolome analysis

Depository of low-molecular-weight compounds or metabolites detected in various organisms in a non-targeted manner is indispensable for metabolomics research. Due to the diverse chemical compounds, various mass spectrometry (MS) setups with state-of-the-art technologies have been used. Over the past two decades, we have analyzed various biological samples by using gas chromatography-mass spectrometry, liquid chromatography-mass spectrometry, or capillary electrophoresis-mass spectrometry, and archived the datasets in the depository MassBase (http://webs2.kazusa.or.jp/massbase/). As the format of MS datasets depends on the MS setup used, we converted each raw binary dataset of the mass chromatogram to text file format, and thereafter, information of the chromatograph peak was extracted in the text file from the converted file. In total, the depository comprises 46,493 datasets, of which 38,750 belong to the plant species and 7,743 are authentic or mixed chemicals as well as other sources (microorganisms, animals, and foods), as on August 1, 2020. All files in the depository can be downloaded in bulk from the website. Mass chromatograms of 90 plant species obtained by LC-Fourier transform ion cyclotron resonance MS or Orbitrap MS, which detect the ionized molecules with high accuracy allowing speculation of chemical compositions, were converted to text files by the software PowerGet, and the chemical annotation of each peak was added. The processed datasets were deposited in the annotation database KomicMarket2 (http://webs2.kazusa.or.jp/km2/). The archives provide fundamental resources for comparative metabolomics and functional genomics, which may result in deeper understanding of living organisms.     

Complete mitochondrial genomes of the Japanese pink coral (Corallium elatius) and the Mediterranean red coral (Corallium rubrum): a reevaluation of the phylogeny of the family Coralliidae based on molecular data

Precious corals are soft corals belonging to the family Coralliidae (Anthozoa: Octocorallia: Alcyonacea) and class Anthozoa, whose skeletal axes are used for jewelry.The family Coralliidae includes ca. 40 species and was originally thought to comprise of the single genus Corallium. In 2003, Corallium was split into two genera, Corallium and Paracorallium, and seven species were moved to this newly identified genus on the bases of morphological features. Previously, we determined the complete mitochondrial genome sequence of two precious corals Paracorallium japonicum and Corallium konojoi, in order to clarify their systematic positions. The two genomes showed high nucleotide sequence identity, but their gene order arrangements were not identical. Here, we determined three complete mitochondrial genome sequences from the one specimen of Mediterranean Corallium rubrum and two specimens of Corallium elatius coming from Kagoshima (South Japan). The circular mitochondrial genomes of C. rubrum and C. elatius are 18,915 bp and 18,969–18,970 bp in length, respectively, and encode 14 typical octocorallian protein-coding genes (nad1–6, nad4L, cox1–3, cob, atp6, atp8, and mtMutS, which is an octocoral-specific mismatch repair gene homologue), two ribosomal RNA genes (rns and rnl), and one transfer RNA (trnM). The overall nucleotide differences between C. konojoi and each C. elatius haplotype (T2007 and I2011) are only 10 and 11 nucleotides, respectively; this degree of similarity indicates that C. elatius and C. konojoi are very closely related species. Notably, the C. rubrum mitochondrial genome shows more nucleotide sequence identity to P. japonicum (99.5%) than to its congeneric species C. konojoi (95.3%) and C. elatius (95.3%). Moreover, the gene order arrangement of C. rubrum was the same as that of P. japonicum, while that of C. elatius was the same as C. konojoi. Phylogenetic analysis based on three mitochondrial genes from 24 scleraxonian species shows that the family Coralliidae is separated into two distinct groups, recovering Corallium as a paraphyletic genus. Our results indicate that the currently accepted generic classification of Coralliidae should be reconsidered.     

Analysis of photosystem II using particle II preparation III. Roles of cytochrome b559 with different redox potentials and plastocyanin in the photosynthetic electron transport system

1. Using the P-II preparation (photosystem II preparation),the functional sites for Cyt-b₅₅₉ with different redox potentialsand for plastocyanin in the non-cyclic electron transport chainof chloroplasts were investigated. 2. In the absence of plastocyanin, the P-II preparation showedno light-induced absorption changes in Cyt-b₅₅₉. However, uponthe addition of a sufficient amount of plastocyanin, remarkablephotooxidation of this cytochrome was observed at room temperature. 3. Parallel measurements of the light-induced absorption changesin both Cyt-b₅₅₉ and plastocyanin revealed a close relationshipbetween them, and indicated that Cyt-b₅₅₉ and plastocyanin arelocated in series on the main path of the electron transportchain involving two photoreactions in PS-II. 4. Difference spectra and action spectra for the light-inducedabsorption changes in Cyt-b₅₅₉ and plastocyanin offered additionalevidence in support of the above conclusion. 5. Analysis of the relationship between the activity of ferricyanideHill reaction and the contents of Cyt-b₅₅₉ of different redoxpotentials showed that both forms of Cyt-b₅₅₉ (i.e. high- andlow-potential forms) play important roles under physiologicalconditions, being on the main pathway of the electron transportchain connecting PS-II and PS-I. 6. To these findings it is possible to give reasonable explanationsbased on our scheme presented previously, which suggested thatPS-II contains not one but two different photoreactions. Thisscheme is much more elaborately supported by this study whichshows the functional sites for Cyt-b₅₅₉ with two different potentials. ¹This work has been supported by a Grant from the Ministry ofEducation (Grant No. 844004), which we gratefully acknowledge.Part of this report has been presented at the Gordon ResearchConference on Regulatory Mechanisms in Photosynthesis, at Tilton,N.H., U.S.A., Aug. 13–17, 1973. (Received June 20, 1974; )