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1. Genomes from Uncultivated Pelagiphages Reveal Multiple Phylogenetic Clades Exhibiting Extensive Auxiliary Metabolic Genes and Cross-Family Multigene Transfers

   https://doi.org/10.1128/msystems.01522-21  

   Wittmers, Fabian ; Needham, David M. ; Hehenberger, Elisabeth ; Giovannoni, Stephen J. ; Worden, Alexandra Z. ( August 2022 , mSystems)

   Rappe, Michael S. (Ed.)

   ABSTRACT For the abundant marine Alphaproteobacterium Pelagibacter (SAR11), and other bacteria, phages are powerful forces of mortality. However, little is known about the most abundant Pelagiphages in nature, such as the widespread HTVC023P-type, which is currently represented by two cultured phages. Using viral metagenomic data sets and fluorescence-activated cell sorting, we recovered 80 complete, undescribed Podoviridae genomes that form 10 phylogenomically distinct clades (herein, named Clades I to X) related to the HTVC023P-type. These expanded the HTVC023P-type pan-genome by 15-fold and revealed 41 previously unknown auxiliary metabolic genes (AMGs) in this viral lineage. Numerous instances of partner-AMGs (colocated and involved in related functions) were observed, including partners in nucleotide metabolism, DNA hypermodification, and Curli biogenesis. The Type VIII secretion system (T8SS) responsible for Curli biogenesis was identified in nine genomes and expanded the repertoire of T8SS proteins reported thus far in viruses. Additionally, the identified T8SS gene cluster contained an iron-dependent regulator (FecR), as well as a histidine kinase and adenylate cyclase that can be implicated in T8SS function but are not within T8SS operons in bacteria. While T8SS are lacking in known Pelagibacter , they contribute to aggregation and biofilm formation in other bacteria. Phylogenetic reconstructions of partner-AMGs indicate derivation from cellular lineages with a more recent transfer between viral families. For example, homologs of all T8SS genes are present in syntenic regions of distant Myoviridae Pelagiphages, and they appear to have alphaproteobacterial origins with a later transfer between viral families. The results point to an unprecedented multipartner-AMG transfer between marine Myoviridae and Podoviridae. Together with the expansion of known metabolic functions, our studies provide new prospects for understanding the ecology and evolution of marine phages and their hosts. IMPORTANCE One of the most abundant and diverse marine bacterial groups is Pelagibacter . Phages have roles in shaping Pelagibacter ecology; however, several Pelagiphage lineages are represented by only a few genomes. This paucity of data from even the most widespread lineages has imposed limits on the understanding of the diversity of Pelagiphages and their impacts on hosts. Here, we report 80 complete genomes, assembled directly from environmental data, which are from undescribed Pelagiphages and render new insights into the manipulation of host metabolism during infection. Notably, the viruses have functionally related partner genes that appear to be transferred between distant viruses, including a suite that encode a secretion system which both brings a new functional capability to the host and is abundant in phages across the ocean. Together, these functions have important implications for phage evolution and for how Pelagiphage infection influences host biology in manners extending beyond canonical viral lysis and mortality. 

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2. Theoretical Predictions Versus Environmental Observations on Serpentinization Fluids: Lessons From the Samail Ophiolite in Oman

   https://doi.org/10.1029/2020JB020756  

   Leong, J. A. M. ; Howells, A. E. ; Robinson, K. J. ; Cox, A. ; Debes, II, R. V. ; Fecteau, K. ; Prapaipong, P. ; Shock, E. L. ( April 2021 , Journal of Geophysical Research: Solid Earth)

   Thermodynamic calculations provide valuable insights into the reactions that drive the profound fluid transformations during serpentinization, where surface fluids are transformed into some of the most reduced and alkaline fluids on Earth. However, environmental observations usually deviate from thermodynamic predictions, especially those occurring at low temperatures where equilibrium is slowly reached. In this work, we analyzed 138 low‐temperature (<40°C) fluids from the Samail ophiolite in Oman to test thermodynamic predictions with environmental observations. Four fluid types were identified through this work. (i) Type 1 circumneutral (pH 7–9) fluids result from fluid interactions with serpentinized rocks common in the shallow subsurface. (ii) Fluids with pH ranging from 9 to 11 and low Si concentrations are products of intermediate stages of serpentinization. (iii) Type 2 hyperalkaline (pH > 11) fluids approach equilibrium with diopside, and with serpentine and brucite actively forming during advanced stages of serpentinization. Lastly, (iv) most fluids sampled in this work deviate from predicted equilibrium compositions and depict various degrees of mixing between Type 1 and 2 fluids. Mixed fluids fall within the same pH range but have considerably higher dissolved Si than intermediate‐type fluids. Hyperalkaline fluids exhibit variable degrees of mixing despite maintaining pH > 11, implying strong buffering capacity of serpentinization‐generated fluids. Overall, this work demonstrates that predicted and measured compositions of serpentinization‐derived fluids can be reconciled using a combination of equilibrium and fluid‐transport simulations. This work substantiates these calculations as useful tools in exploring serpentinization reactions in continents and perhaps in other low‐temperature environments on Earth and beyond.

    

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3. Electrocatalytic Conversion of Furanic Compounds for Production of Valuable Chemicals

   Li, Wenzhen ; Chadderdon, Xiaotong ; Chadderdon, David ; Liu, Hengzhou ( August 2021 , 72nd International Society of Electrochemistry Meeting)

   Biomass is abundant, inexpensive and renewable, therefore, it is highly expected to play a significant role in our future energy and chemical landscapes. The US DOE has identified furanic compounds (furfural and 5-(hydroxymethyl)furfural (HMF)) as the top platform building-block chemicals that can be readily derived from biomass sources [1]. Electrocatalytic conversion of these furanic compounds is an emerging route for the sustainable production of valuable chemicals [2, 3]. In my presentation, I will first present our recent mechanistic study of electrochemical reduction of furfural through a combination of voltammetry, preparative electrolysis, thiol-electrode modifications, and kinetic isotope studies [4]. It is demonstrated that two distinct mechanisms are operable on metallic Cu electrodes in acidic electrolytes: (i) electrocatalytic hydrogenation (ECH) and (ii) direct electroreduction. The contributions of each mechanism to the observed product distribution are clarified by evaluating the requirement for direct chemical interactions with the electrode surface and the role of adsorbed hydrogen. Further analysis reveals that hydrogenation and hydrogenolysis products are generated by parallel ECH pathways. Understanding the underlying mechanisms enables the manipulation of furfural reduction by rationally tuning the electrode potential, electrolyte pH, and furfural concentration to promote selective formation of important bio-based polymer precursors and fuels. Next, I will present electrocatalytic conversion of HMF to two biobased monomers in an H-type electrochemical cell [5]. HMF reduction (hydrogenation) to 2,5-bis(hydroxymethyl)furan (BHMF) was achieved under mild electrolyte conditions and ambient temperature using a Ag/C cathode. Meanwhile, HMF oxidation to 2,5-furandicarboxylic acid (FDCA) with ~100% efficiency was facilitated under the same conditions by a homogeneous nitroxyl radical redox mediator, together with an inexpensive carbon felt anode. The selectivity and efficiency for Ag-catalyzed BHMF formation were sensitive to cathode potential, owing to competition from HMF hydrodimerization reactions and water reduction (hydrogen evolution). Moreover, the carbon support of Ag/C was active for HMF reduction and contributed to undesired dimer/oligomer formation at strongly cathodic potentials. As a result, high BHMF selectivity and efficiency were only achieved within a narrow potential range near –1.3 V. Fortunately, the selectivity of redox-mediated HMF oxidation was insensitive to anode potential, thus allowing HMF hydrogenation and oxidation half reactions to be performed together in a single cathode-potential-controlled cell. Electrocatalytic HMF conversion in a paired cell achieved high molar yields of BHMF and FDCA, and nearly doubled electron efficiency compared to the unpaired cell. Finally, I will briefly introduce our recent work on the development of a three-electrode flow cell with an oxide-derived Ag (OD-Ag) cathode and catbon felt anode for paring elecatalytic oxidation and reduction of HMF. The flow cell has a remarkable cell voltage reduction from ~7.5 V to ~2.0 V by transferring the electrolysis from the H-type cell to the flow cell [6]. This represents a more than fourfold increase in the energy efficiency at the 10 mA operation. A combined faradaic efficiency of 163% was obtained to BHMF and FDCA. Alternatively, the anodic hydrogen oxidation reaction on platinum further reduced the cell voltage to only ~0.85 V at 10 mA operation. These paired processes have shown potential for integrating renewable electricity and carbon for distributed chemical manufacturing in the future. 

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4. Mixed ancestry and admixture in Kauai's feral chickens: invasion of domestic genes into ancient Red Junglefowl reservoirs

   https://doi.org/10.1111/mec.13096  

   Gering, E. ; Johnsson, M. ; Willis, P. ; Getty, T. ; Wright, D. ( March 2015 , Molecular Ecology)

   A major goal of invasion genetics is to determine how establishment histories shape non‐native organisms' genotypes and phenotypes. While domesticated species commonly escape cultivation to invade feral habitats, few studies have examined how this process shapes feral gene pools and traits. We collected genomic and phenotypic data from feral chickens (Gallus gallus) on the Hawaiian island of Kauai to (i) ascertain their origins and (ii) measure standing variation in feral genomes, morphology and behaviour. Mitochondrial phylogenies (D‐loop & whole Mt genome) revealed two divergent clades within our samples. The rare clade also contains sequences from Red Junglefowl (the domestic chicken's progenitor) and ancientDNAsequences from Kauai that predate European contact. This lineage appears to have been dispersed into the east Pacific by ancient Polynesian colonists. The more prevalent MtDNAclade occurs worldwide and includes domesticated breeds developed recently in Europe that are farmed within Hawaii. We hypothesize this lineage originates from recently feralized livestock and found supporting evidence for increasedG. gallusdensity on Kauai within the last few decades.SNPs obtained from whole‐genome sequencing were consistent with historic admixture between Kauai's divergent(G. gallus)lineages. Additionally, analyses of plumage, skin colour and vocalizations revealed that Kauai birds' behaviours and morphologies overlap with those of domestic chickens and Red Junglefowl, suggesting hybrid origins. Together, our data support the hypotheses that (i) Kauai's feralG. gallusdescend from recent invasion(s) of domestic chickens into an ancient Red Junglefowl reservoir and (ii) feral chickens exhibit greater phenotypic diversity than candidate source populations. These findings complicate management objectives for Pacific feral chickens, while highlighting the potential of this and other feral systems for evolutionary studies of invasions.

    

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5. Reconstructing Genomes of Carbon Monoxide Oxidisers in Volcanic Deposits Including Members of the Class Ktedonobacteria

   https://doi.org/10.3390/microorganisms8121880  

   Hernández, Marcela ; Vera-Gargallo, Blanca ; Calabi-Floody, Marcela ; King, Gary M. ; Conrad, Ralf ; Tebbe, Christoph C. ( December 2020 , Microorganisms)

   null (Ed.)

   Microorganisms can potentially colonise volcanic rocks using the chemical energy in reduced gases such as methane, hydrogen (H2) and carbon monoxide (CO). In this study, we analysed soil metagenomes from Chilean volcanic soils, representing three different successional stages with ages of 380, 269 and 63 years, respectively. A total of 19 metagenome-assembled genomes (MAGs) were retrieved from all stages with a higher number observed in the youngest soil (1640: 2 MAGs, 1751: 1 MAG, 1957: 16 MAGs). Genomic similarity indices showed that several MAGs had amino-acid identity (AAI) values >50% to the phyla Actinobacteria, Acidobacteria, Gemmatimonadetes, Proteobacteria and Chloroflexi. Three MAGs from the youngest site (1957) belonged to the class Ktedonobacteria (Chloroflexi). Complete cellular functions of all the MAGs were characterised, including carbon fixation, terpenoid backbone biosynthesis, formate oxidation and CO oxidation. All 19 environmental genomes contained at least one gene encoding a putative carbon monoxide dehydrogenase (CODH). Three MAGs had form I coxL operon (encoding the large subunit CO-dehydrogenase). One of these MAGs (MAG-1957-2.1, Ktedonobacterales) was highly abundant in the youngest soil. MAG-1957-2.1 also contained genes encoding a [NiFe]-hydrogenase and hyp genes encoding accessory enzymes and proteins. Little is known about the Ktedonobacterales through cultivated isolates, but some species can utilise H2 and CO for growth. Our results strongly suggest that the remote volcanic sites in Chile represent a natural habitat for Ktedonobacteria and they may use reduced gases for growth. 

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