Complete genome sequence of Arcanobacterium haemolyticum type strain (11018)

Arcanobacterium haemolyticum (ex MacLean et al. 1946) Collins et al. 1983 is the type species of the genus Arcanobacterium, which belongs to the family Actinomycetaceae. The strain is of interest because it is an obligate parasite of the pharynx of humans and farm animal; occasionally, it causes pharyngeal or skin lesions. It is a Gram-positive, nonmotile and non-sporulating bacterium. The strain described in this study was isolated from infections amongst American soldiers of certain islands of the North and West Pacific. This is the first completed sequence of a member of the genus Arcanobacterium and the ninth type strain genome from the family Actinomycetaceae. The 1,986,154 bp long genome with its 1,821 protein-coding and 64 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Insights from protein-protein interaction studies on bacterial pathogenesis

Introduction: The threat bacterial pathogens pose to human health is increasing with the number and distribution of antibiotic-resistant bacteria, while the rate of discovery of new antimicrobials dwindles. Proteomics is playing key roles in understanding the molecular mechanisms of bacterial pathogenesis, and in identifying disease outcome determinants. The physical associations identified by proteomics can provide the means to develop pathogen-specific treatment methods that reduce the spread of antibiotic resistance and alleviate the negative effects of broad-spectrum antibiotics on beneficial bacteria.

Areas covered: This review discusses recent trends in proteomics and introduces new and developing approaches that can be applied to the study of protein-protein interactions (PPIs) underlying bacterial pathogenesis. The approaches examined encompass options for mapping proteomes as well as stable and transient interactions in vivo and in vitro. We also explored the coverage of bacterial and human-bacterial PPIs, knowledge gaps in this area, and how they can be filled.

Expert commentary: Identifying potential antimicrobial candidates is confounded by the complex molecular biology of bacterial pathogenesis and the lack of knowledge about PPIs underlying this process. Proteomics approaches can offer new perspectives for mechanistic insights and identify essential targets for guiding the discovery of next generation antimicrobials.     

Comparison of methane, nitrous oxide fluxes and CO2 respiration rates from a Mediterranean cork oak ecosystem and improved pasture

Background and aims

During the recent decades, cork oak (Q. suber) mortality has been increasing in Mediterranean oak woodland endangering the economical and environmental sustainability of the “montado” ecosystem. This fact in combination with climate change and conversion of forestland to pasture may significantly affect the soil-atmosphere greenhouse gases (GHGs) exchange. Our study evaluates the impact of oak trees as compared to pasture on net ecosystem GHG (CH_4, N₂O, and CO₂) exchange as well as the main environmental factors influencing this exchange.

Methods

We used field chamber measurements for the collection of GHGs under three different conditions: 1) open area (OA), 2) under tree canopy area (UC) and 3) improved pasture (IP). Experiments were done under typical Mediterranean climate at central Portugal in 2010 and 2011.

Results

The UC had higher nitrification potential, soil C/N ratio, electrical conductivity, litter input and soil organic matter (SOM) than OA and IP. SOM positively correlated with soil CH₄ and N₂O fluxes but not with soil CO₂ respiration rates. Soil water content (SWC) drives both CH₄ and N₂O fluxes. Under certain conditions, when SWC reached a threshold (7 % for CH₄ and 3 % for N₂O) the result was net uptake and that net uptake increased with SWC. This was the case for the UC and OA. Conversely, for the IP soil water content above 4 % promoted net CH₄ release.

Conclusions

Our results show that cork oak influences soil properties and consequently GHGs fluxes. In the UC the input of litter for SOM together with soil moisture, favoured microbiological activity and related GHGs fluxes. Soil temperature is a secondary factor in the studied conditions. Our results also emphasized the potential impact posed by decreased cork oak tree density in the functioning of the “montado” ecosystem.     

Complete genome sequence of the aerobic marine methanotroph Methylomonas methanica MC09

Methylomonas methanica MC09 is a mesophilic, halotolerant, aerobic, methanotrophic member of the Gammaproteobacteria, isolated from coastal seawater. Here we present the complete genome sequence of this strain, the first available from an aerobic marine methanotroph.     

Complete genome sequence and updated annotation of Desulfovibrio alaskensis G20

Desulfovibrio alaskensis G20 (formerly Desulfovibrio desulfuricans G20) is a Gram-negative mesophilic sulfate-reducing bacterium (SRB), known to corrode ferrous metals and to reduce toxic radionuclides and metals such as uranium and chromium to sparingly soluble and less toxic forms. We present the 3.7-Mb genome sequence to provide insights into its physiology.     

High-density lipoprotein remodeling affects the osmotic properties of plasma in goldfish under critical salinity

To investigate the stress response and physiological adaptations of goldfish (Carassius auratus) to critical salinity (CS) waters, we analyzed high-density lipoprotein (HDL) stoichiometry, stress markers (cortisol, glucose), and plasma osmotic properties (Na⁺, osmolality, water content) using ichthyology, biochemistry, and proteomics approaches. After 21 days of exposure to CS, plasma concentrations of cortisol, glucose, and Na⁺ increased, indicating stress. Total plasma osmolality (Osm_total) and osmolality generated by inorganic (Osm_inorg) and organic osmolytes (Osm_org) also increased, the latter by ~2%. We associated the increase of Osm_org with (1) increased metabolite concentration (glucose), (2) dissociation of HDL particles resulting in increased HDL number per unit plasma volume (~1.5–2-fold) and (3) increased HDL osmotic activity. HDL remodeling may be the reason for the redistribution of bound and free water in plasma, which may contribute to water retention in plasma and, at the same time, to hemodynamic disturbances under CS conditions. The study's findings suggest that HDL remodeling is an important mechanism for maintaining osmotic homeostasis in fish, which is consistent with current capillary exchange models in vertebrates.     

Phylogeography of northern Dolly Varden Salvelinus malma malma based on analysis of mitochondrial DNA

The northern Dolly Varden, Salvelinus malma malma, is a typical representative of arctic fauna distributed in northeastern Asia and northwestern North America. Because its spawning habitats were affected by Pleistocene glacial advances over most of its natural range, S. m. malma is among the most interesting objects of phylogeographic and microevolutionary studies. We reconstructed the genealogy of mtDNA haplotypes from 27 Alaskan and Asian populations to study the influence of glacial and geological vicariance events on the contemporary population genetic structure, phylogeographic subdivision and distribution of the northern Dolly Varden. Analysis of restriction site states in three PCR‐amplified mtDNA regions (ND1/ND2, ND5/ND6, Cytb/D‐loop; 47% of the mitochondrial genome) resolved 75 haplotypes in 436 fish. Similar patterns of subspecific variation apparent from hierarchical diversity and nested clade analyses of mtDNA haplotypes identify weak spatial differentiation and low levels of divergence. Our results suggest that (1) demographic history has been influenced by historical range expansions and recent isolation by distance, (2) present populations from Asia and North America were colonized from one main Beringian Refugium, and (3) that this taxon's ancestral population probably experienced a bottleneck in the Beringian Refugium during the late Pleistocene (Wisconsin) glacial period.