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1. Syntrophotalea acetylenivorans sp. nov., a diazotrophic, acetylenotrophic anaerobe isolated from intertidal sediments

   https://doi.org/10.1099/ijsem.0.004698  

   Baesman, Shaun M; Sutton, John M; Fierst, Janna L; Akob, Denise M; Oremland, Ronald S (June 2019, International Journal of Systematic and Evolutionary Microbiology)

   A Gram-stain-negative, strictly anaerobic, non-motile, rod-shaped bacterium, designated SFB93^T, was isolated from the intertidal sediments of South San Francisco Bay, located near Palo Alto, CA, USA. SFB93^Twas capable of acetylenotrophic and diazotrophic growth, grew at 22–37 °C, pH 6.3–8.5 and in the presence of 10–45 g l⁻¹NaCl. Phylogenetic analyses based on 16S rRNA gene sequencing showed that SFB93^Trepresented a member of the genusSyntrophotaleawith highest 16S rRNA gene sequence similarities toSyntrophotalea acetylenicaDSM 3246^T(96.6 %),Syntrophotalea carbinolicaDSM 2380^T(96.5 %), andSyntrophotalea venetianaDSM 2394^T(96.7 %). Genome sequencing revealed a genome size of 3.22 Mbp and a DNA G+C content of 53.4 %. SFB93^Thad low genome-wide average nucleotide identity (81–87.5 %) and <70 % digital DNA–DNA hybridization value with other members of the genusSyntrophotalea. The phylogenetic position of SFB93^Twithin the familySyntrophotaleaceaeand as a novel member of the genusSyntrophotaleawas confirmed via phylogenetic reconstruction based on concatenated alignments of 92 bacterial core genes. On the basis of the results of phenotypic, genotypic and phylogenetic analyses, a novel species,Syntrophotalea acetylenivoranssp. nov., is proposed, with SFB93^T(=DSM 106009^T=JCM 33327^T=ATCC TSD-118^T) as the type strain. 

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2. Vibrio floridensis sp. nov., a novel species closely related to the human pathogen Vibrio vulnificus isolated from a cyanobacterial bloom

   https://doi.org/10.1099/ijsem.0.005675  

   Grant, Trudy-Ann; Jayakumar, Jane M.; López-Pérez, Mario; Almagro-Moreno, Salvador (February 2023, International Journal of Systematic and Evolutionary Microbiology)

   A Gram-stain-negative, rod-shaped bacterial strain, designatedVibrio floridensisIRLE0018 (=NRRL B-65642=NCTC 14661), was isolated from a cyanobacterial bloom along the Indian River Lagoon (IRL), a large and highly biodiverse estuary in eastern Florida (USA). The results of phylogenetic, biochemical, and phenotypic analyses indicate that this isolate is distinct from species of the genusVibriowith validly published names and is the closest relative to the emergent human pathogen,Vibrio vulnificus. Here, we present the complete genome sequence ofV. floridensisstrain IRLE0018 (4 535 135 bp). On the basis of the established average nucleotide identity (ANI) values for the determination of different species (ANI <95 %), strain IRLE0018, with an ANI of approximately 92 % compared with its closest relative,V. vulnificus, represents a novel species within the genusVibrio. To our knowledge, this represents the first time this species has been described. The results of genomic analyses ofV. floridensisIRLE0018 indicate the presence of antibiotic resistance genes and several known virulence factors, however, its pathogenicity profile (e.g. survival in serum, phagocytosis avoidance) reveals limited virulence potential of this species in contrast toV. vulnificus. 

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3. On the Support of Anomalous Dissipation Measures

   https://doi.org/10.1007/s00021-024-00894-z  

   De_Rosa, Luigi; Drivas, Theodore D; Inversi, Marco (November 2024, Journal of Mathematical Fluid Mechanics)

   Abstract By means of a unifying measure-theoretic approach, we establish lower bounds on the Hausdorff dimension of the space-time set which can support anomalous dissipation for weak solutions of fluid equations, both in the presence or absence of a physical boundary. Boundary dissipation, which can occur at both the time and the spatial boundary, is analyzed by suitably modifying the Duchon & Robert interior distributional approach. One implication of our results is that any bounded Euler solution (compressible or incompressible) arising as a zero viscosity limit of Navier–Stokes solutions cannot have anomalous dissipation supported on a set of dimension smaller than that of the space. This result is sharp, as demonstrated by entropy-producing shock solutions of compressible Euler (Drivas and Eyink in Commun Math Phys 359(2):733–763, 2018.https://doi.org/10.1007/s00220-017-3078-4; Majda in Am Math Soc 43(281):93, 1983.https://doi.org/10.1090/memo/0281) and by recent constructions of dissipative incompressible Euler solutions (Brue and De Lellis in Commun Math Phys 400(3):1507–1533, 2023.https://doi.org/10.1007/s00220-022-04626-0 624; Brue et al. in Commun Pure App Anal, 2023), as well as passive scalars (Colombo et al. in Ann PDE 9(2):21–48, 2023.https://doi.org/10.1007/s40818-023-00162-9; Drivas et al. in Arch Ration Mech Anal 243(3):1151–1180, 2022.https://doi.org/10.1007/s00205-021-01736-2). For$$L^q_tL^r_x$$ $L_t^q{L}_x^r$suitable Leray–Hopf solutions of the$$d-$$ $d-$dimensional Navier–Stokes equation we prove a bound of the dissipation in terms of the Parabolic Hausdorff measure$$\mathcal {P}^{s}$$ $P^s$, which gives$$s=d-2$$ $s=d-2$as soon as the solution lies in the Prodi–Serrin class. In the three-dimensional case, this matches with the Caffarelli–Kohn–Nirenberg partial regularity. 

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4. Reference-agnostic representation and visualization of pan-genomes

   https://doi.org/10.1186/s12859-021-04424-w  

   Liang, Qihua; Lonardi, Stefano (October 2021, BMC Bioinformatics)

   Abstract BackgroundThe pan-genome of a species is the union of the genes and non-coding sequences present in all individuals (cultivar, accessions, or strains) within that species. ResultsHere we introduce PGV, a reference-agnostic representation of the pan-genome of a species based on the notion of consensus ordering. Our experimental results demonstrate that PGV enables an intuitive, effective and interactive visualization of a pan-genome by providing a genome browser that can elucidate complex structural genomic variations. ConclusionsThe PGV software can be installed via conda or downloaded fromhttps://github.com/ucrbioinfo/PGV. The companion PGV browser athttp://pgv.cs.ucr.educan be tested using example bed tracks available from the GitHub page. 

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5. A global perspective on bacterial diversity in the terrestrial deep subsurface

   https://doi.org/10.1099/mic.0.001172  

   Soares, A; Edwards, A; An, D; Bagnoud, A; Bradley, J; Barnhart, E; Bomberg, M; Budwill, K; Caffrey, S M; Fields, M; et al (January 2023, Microbiology)

   While recent efforts to catalogue Earth’s microbial diversity have focused upon surface and marine habitats, 12–20 % of Earth’s biomass is suggested to exist in the terrestrial deep subsurface, compared to ~1.8 % in the deep subseafloor. Metagenomic studies of the terrestrial deep subsurface have yielded a trove of divergent and functionally important microbiomes from a range of localities. However, a wider perspective of microbial diversity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated byBetaproteobacteria, GammaproteobacteriaandFirmicutes, probably as a function of the diverse metabolic strategies of these taxa. Evidence was also found for a common small consortium of prevalentBetaproteobacteriaandGammaproteobacteriaoperational taxonomic units across the localities. This implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, depth and other variables, that may play an important role in colonizing and sustaining microbial habitats in the deep terrestrial subsurface. Anin silicocontamination-aware approach to analysing this dataset underscores the importance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial diversity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling. 

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