Ethanolamine metabolism through two genetically distinct loci enables Klebsiella pneumoniae to bypass nutritional competition in the gut.

Successful microbial colonization of the gastrointestinal (GI) tract hinges on an organism's ability to overcome the intense competition for nutrients in the gut between the host and the resident gut microbiome. Enteric pathogens can exploit ethanolamine (EA) in the gut to bypass nutrient competition. However, Klebsiella pneumoniae (K. pneumoniae) is an asymptomatic gut colonizer and, unlike well-studied enteric pathogens, harbors two genetically distinct ethanolamine utilization (eut) loci. Our investigation uncovered unique roles for each eut locus depending on EA utilization as a carbon or nitrogen source. Murine gut colonization studies demonstrated the necessity of both eut loci in the presence of intact gut microbiota for robust GI colonization by K. pneumoniae. Additionally, while some Escherichia coli gut isolates could metabolize EA, other commensals were incapable, suggesting that EA metabolism likely provides K. pneumoniae a selective advantage in gut colonization. Molecular and bioinformatic analyses unveiled the conservation of two eut loci among K. pneumoniae and a subset of the related taxa in the K. pneumoniae species complex, with the NtrC-RpoN regulatory cascade playing a pivotal role in regulation. These findings identify EA metabolism as a critical driver of K. pneumoniae niche establishment in the gut and propose microbial metabolism as a potential therapeutic avenue to combat K. pneumoniae infections.

Deciphering the gastrointestinal carriage of Klebsiella pneumoniae.

Bacterial infections pose a significant global health threat, accounting for an estimated 7.7 million deaths. Hospital outbreaks driven by multi-drug-resistant pathogens, notably Klebsiella pneumoniae (K. pneumoniae), are of grave concern. This opportunistic pathogen causes pneumonia, urinary tract infections, and bacteremia, particularly in immunocompromised individuals. The rise of hypervirulent K. pneumoniae adds complexity, as it increasingly infects healthy individuals. Recent epidemiological data suggest that asymptomatic gastrointestinal carriage serves as a reservoir for infections in the same individual and allows for host-to-host transmission via the fecal-oral route. This review focuses on K. pneumoniae's gastrointestinal colonization, delving into epidemiological evidence, current animal models, molecular colonization mechanisms, and the protective role of the resident gut microbiota. Moreover, the review sheds light on in vivo high-throughput approaches that have been crucial for identifying K. pneumoniae factors in gut colonization. This comprehensive exploration aims to enhance our understanding of K. pneumoniae gut pathogenesis, guiding future intervention and prevention strategies.

Long-term organic carbon preservation enhanced by iron and manganese.

The balance between degradation and preservation of sedimentary organic carbon (OC) is important for global carbon and oxygen cycles1. The relative importance of different mechanisms and environmental conditions contributing to marine sedimentary OC preservation, however, remains unclear2-8. Simple organic molecules can be geopolymerized into recalcitrant forms by means of the Maillard reaction5, although reaction kinetics at marine sedimentary temperatures are thought to be slow9,10. More recent work in terrestrial systems suggests that the reaction can be catalysed by manganese minerals11-13, but the potential for the promotion of geopolymerized OC formation at marine sedimentary temperatures is uncertain. Here we present incubation experiments and find that iron and manganese ions and minerals abiotically catalyse the Maillard reaction by up to two orders of magnitude at temperatures relevant to continental margins where most preservation occurs4. Furthermore, the chemical signature of the reaction products closely resembles dissolved and total OC found in continental margin sediments globally. With the aid of a pore-water model14, we estimate that iron- and manganese-catalysed transformation of simple organic molecules into complex macromolecules might generate on the order of approximately 4.1 Tg C yr-1 for preservation in marine sediments. In the context of perhaps only about 63 Tg C yr-1 variation in sedimentary organic preservation over the past 300 million years6, we propose that variable iron and manganese inputs to the ocean could exert a substantial but hitherto unexplored impact on global OC preservation over geological time.

Response of soil bacterial populations to application of biosolids under short-term flooding.

Biosolids are applied to agricultural land as a soil conditioner and source of crop nutrients. However, there is concern that bacteria from biosolids may become established in soils, particularly if that soil becomes water-logged. This study examined the microbial community of arable soils cultivated with barley under different applications of biosolids (0, 24t/ha, 48t/ha) in laboratory mesocosms which simulated a 10-day flood. Nutrients (P and N) and organic matter in the soil increased with application rate, but plant growth was not affected by biosolid application. The biosolids contained 10× more genetic material than the soil, with much lower bacterial diversity, yet application did not significantly change the taxonomy of the soil microbiome, with minor changes related to increased nutrients and SOM. Anaerobic conditions developed rapidly during flooding, causing shifts in the native soil microbiome. Some bacterial taxa that were highly abundant in biosolids had slightly increased relative abundance in amended soils during the flood. After flooding, soil bacterial populations returned to their pre-flood profiles, implying that the native microbial community is resilient to transient changes. The short-term changes in the microbiome of biosolid-amended soils during flooding do not appear to increase the environmental risk posed by biosolid application.

Klebsiella pneumoniae l-Fucose Metabolism Promotes Gastrointestinal Colonization and Modulates Its Virulence Determinants.

Colonization of the gastrointestinal (GI) tract by Klebsiella pneumoniae is generally considered asymptomatic. However, gut colonization allows K. pneumoniae to either translocate to sterile site within the same host or transmit through the fecal-oral route to another host. K. pneumoniae gut colonization is poorly understood, but knowledge of this first step toward infection and spread is critical for combatting its disease manifestations. K. pneumoniae must overcome colonization resistance (CR) provided by the host microbiota to establish itself within the gut. One such mechanism of CR is through nutrient competition. Pathogens that metabolize a broad range of substrates have the ability to bypass nutrient competition and overcome CR. Herein, we demonstrate that in response to mucin-derived fucose, the conserved fucose metabolism operon (fuc) of K. pneumoniae is upregulated in the murine gut, and we subsequently show that fucose metabolism promotes robust gut colonization. Growth studies using cecal filtrate as a proxy for the gut lumen illustrate the growth advantage that the fuc operon provides K. pneumoniae. We further show that fucose metabolism allows K. pneumoniae to be competitive with a commensal Escherichia coli isolate (Nissle). However, Nissle is eventually able to outcompete K. pneumoniae, suggesting that it can be utilized to enhance CR. Finally, we observed that fucose metabolism positively modulates hypermucoviscosity, autoaggregation, and biofilm formation but not capsule biogenesis. Together, these insights enhance our understanding of the role of alternative carbon sources in K. pneumoniae gut colonization and the complex relationship between metabolism and virulence in this species.

MgrB-Dependent Colistin Resistance in Klebsiella pneumoniae Is Associated with an Increase in Host-to-Host Transmission.

Due to its high transmissibility, Klebsiella pneumoniae is one of the leading causes of nosocomial infections. Here, we studied the biological cost of colistin resistance, an antibiotic of last resort, in this opportunistic pathogen using a murine model of gut colonization and transmission. Colistin resistance in K. pneumoniae is commonly the result of the inactivation of the small regulatory protein MgrB. Without a functional MgrB, the two-component system PhoPQ is constitutively active, leading to an increase in lipid A modifications and subsequent colistin resistance. Using an isogenic mgrB deletion mutant (MgrB-), we demonstrate that the mutant's colistin resistance is not associated with a fitness defect under in vitro growth conditions. However, in our murine model of K. pneumoniae gastrointestinal (GI) colonization, the MgrB- colonizes the gut poorly, allowing us to identify a fitness cost. Moreover, the MgrB- mutant has higher survival outside the host compared with the parental strain. We attribute this enhanced survivability to dysregulation of the PhoPQ two-component system and accumulation of the master stress regulator RpoS. The enhanced survival of MgrB- may be critical for its rapid host-to-host transmission observed in our model. Together, our data using multiple clinical isolates demonstrate that MgrB-dependent colistin resistance in K. pneumoniae comes with a biological cost in gut colonization. However, this cost is mitigated by enhanced survival outside the host and consequently increases its host-to-host transmission. Additionally, it underscores the importance of considering the entire life cycle of a pathogen to determine the actual biological cost associated with antibiotic resistance. IMPORTANCE The biological cost associated with colistin resistance in Klebsiella pneumoniae was examined using a murine model of K. pneumoniae gut colonization and fecal-oral transmission. A common mutation resulting in colistin resistance in K. pneumoniae is a loss-of-function mutation of the small regulatory protein MgrB that regulates the two-component system PhoPQ. Even though colistin resistance in K. pneumoniae comes with a fitness defect in gut colonization, it increases bacterial survival outside the host enabling it to transmit more effectively to a new host. The enhanced survival is dependent upon the accumulation of RpoS and dysregulation of the PhoPQ. Hence, our study expands our understanding of the underlying molecular mechanism contributing to the transmission of colistin-resistant K. pneumoniae.

Animal Model To Study Klebsiella pneumoniae Gastrointestinal Colonization and Host-to-Host Transmission.

An important yet poorly understood facet of the life cycle of a successful pathogen is host-to-host transmission. Hospital-acquired infections (HAI) resulting from the transmission of drug-resistant pathogens affect hundreds of millions of patients worldwide. Klebsiella pneumoniae, a Gram-negative bacterium, is notorious for causing HAI, with many of these infections difficult to treat, as K. pneumoniae has become multidrug resistant. Epidemiological studies suggest that K. pneumoniae host-to-host transmission requires close contact and generally occurs through the fecal-oral route. Here, we describe a murine model that can be utilized to study mucosal (oropharynx and gastrointestinal [GI]) colonization, shedding within feces, and transmission of K. pneumoniae through the fecal-oral route. Using an oral route of inoculation, and fecal shedding as a marker for GI colonization, we showed that K. pneumoniae can asymptomatically colonize the GI tract in immunocompetent mice and modifies the host GI microbiota. Colonization density within the GI tract and levels of shedding in the feces differed among the clinical isolates tested. A hypervirulent K. pneumoniae isolate was able to translocate from the GI tract and cause hepatic infection that mimicked the route of human infection. Expression of the capsule was required for colonization and, in turn, robust shedding. Furthermore, K. pneumoniae carrier mice were able to transmit to uninfected cohabitating mice. Lastly, treatment with antibiotics led to changes in the host microbiota and development of a transient supershedder phenotype, which enhanced transmission efficiency. Thus, this model can be used to determine the contribution of host and bacterial factors toward K. pneumoniae dissemination.

Multiple hyperpigmented papules and plaques.

We had our suspicions as to the diagnosis, but a particular sign was missing. The biopsy settled things.

Atmospheric Carbon Capture Performance of Legacy Iron and Steel Waste.

Legacy iron (Fe) and steel wastes have been identified as a significant source of silicate minerals, which can undergo carbonation reactions and thus sequester carbon dioxide (CO2). In reactor experiments, i.e., at elevated temperatures, pressures, or CO2 concentrations, these wastes have high silicate to carbonate conversion rates. However, what is less understood is whether a more "passive" approach to carbonation can work, i.e., whether a traditional slag emplacement method (heaped and then buried) promotes or hinders CO2 sequestration. In this paper, the results of characterization of material retrieved from a first of its kind drilling program on a historical blast furnace slag heap at Consett, U.K., are reported. The mineralogy of the slag material was near uniform, consisting mainly of melilite group minerals with only minor amounts of carbonate minerals detected. Further analysis established that total carbon levels were on average only 0.4% while average calcium (Ca) levels exceeded 30%. It was calculated that only ∼3% of the CO2 sequestration potential of the >30 Mt slag heap has been utilized. It is suggested that limited water and gas interaction and the mineralogy and particle size of the slag are the main factors that have hindered carbonation reactions in the slag heap.

Abiotic reduction of Cr(VI) by humic acids derived from peat and lignite: kinetics and removal mechanism.

Hexavalent chromium contamination of groundwater is a worldwide problem caused by anthropogenic and natural processes. We report the rate of Cr(VI) removal by two humic acids (extracted from Miocene age lignite and younger peat soil) in aqueous suspensions across a pH range likely to be encountered in terrestrial environments. Cr(VI) was reduced to Cr(III) in a first-order reaction with respect Cr(VI) concentration, but exhibited a partial order (~ 0.5) with respect to [H+]. This reaction was more rapid with the peat humic acid, where Cr(VI) reduction was observed at all pH values investigated (3.7 ≤ pH ≤ 10.5). 13C NMR and pyrolysis GC-MS spectroscopy indicate that the reaction results in loss of substituted phenolic moieties and hydroxyl groups from the humic acids. X-ray absorption spectroscopy indicated that at all pH values the resulting Cr(III) was associated with the partially degraded humic acid in an inner-sphere adsorption complex. The reaction mechanism is likely to be controlled by ester formation between Cr(VI) and phenolic/hydroxyl moieties, as this initial step is rapid in acidic systems but far less favourable in alkaline conditions. Our findings highlight the potential of humic acid to reduce and remove Cr(VI) from solution in a range of environmental conditions.

Behaviour and fate of vanadium during the aerobic neutralisation of hyperalkaline slag leachate.

Vanadium is a toxic metal present in alkaline leachates produced during the weathering of steel slags. Slag leaching can therefore have deleterious effects on local watercourses due to metal toxicity, the effects of the high pH (9-12.5) and rapid carbonation (leading to smothering of benthic communities). We studied the fate and behaviour of V in slag leachate both through field observations of a heavily affected stream (Howden Burn, Consett UK) and in controlled laboratory experiments where slag leachates were neutralised by CO2 ingassing from air. V was found to be removed from leachates downstream from the Howden Burn source contemporaneously with a fall in pH, Ca, Al and Fe concentrations. In the neutralisation experiments pH reduced from 12 → 8, and limited quantities of V were incorporated into precipitated CaCO3. The presence of kaolinite clay (i.e. SiOH and AlOH surfaces) during neutralisation experiments had no measureable effect on V uptake in the alkaline to circumneutral pH range. XANES analysis showed that V was present in precipitates recovered from experiments as adsorbed or incorporated V(V) indicating its likely presence in leachates as the vanadate oxyanion (HVO42-). Nano-scale particles of 2-line ferrihydrite also formed in the neutralised leachates potentially providing an additional sorption surface for V uptake. Indeed, removal of V from leachates was significantly enhanced by the addition of goethite (i.e. FeOOH surfaces) to experiments. EXAFS analysis of recovered goethite samples showed HVO42- was adsorbed by the formation of strong inner-sphere complexes, facilitating V removal from solution at pH < 10. Results show that carbonate formation leads to V removal from leachates during leachate neutralisation, and the presence of both naturally occurring and neoformed Fe (oxy)hydroxides provide a potent sink for V in slag leachates, preventing the spread of V in the environment.

Hydration of dicalcium silicate and diffusion through neo-formed calcium-silicate-hydrates at weathered surfaces control the long-term leaching behaviour of basic oxygen furnace (BOF) steelmaking slag.

Alkalinity generation and toxic trace metal (such as vanadium) leaching from basic oxygen furnace (BOF) steel slag particles must be properly understood and managed by pre-conditioning if beneficial reuse of slag is to be maximised. Water leaching under aerated conditions was investigated using fresh BOF slag at three different particle sizes (0.5-1.0, 2-5 and 10 × 10 × 20 mm blocks) and a 6-month pre-weathered block. There were several distinct leaching stages observed over time associated with different phases controlling the solution chemistry: (1) free-lime (CaO) dissolution (days 0-2); (2) dicalcium silicate (Ca2SiO4) dissolution (days 2-14) and (3) Ca-Si-H and CaCO3 formation and subsequent dissolution (days 14-73). Experiments with the smallest size fraction resulted in the highest Ca, Si and V concentrations, highlighting the role of surface area in controlling initial leaching. After ~2 weeks, the solution Ca/Si ratio (0.7-0.9) evolved to equal those found within a Ca-Si-H phase that replaced dicalcium silicate and free-lime phases in a 30- to 150-µm altered surface region. V release was a two-stage process; initially, V was released by dicalcium silicate dissolution, but V also isomorphically substituted for Si into the neo-formed Ca-Si-H in the alteration zone. Therefore, on longer timescales, the release of V to solution was primarily controlled by considerably slower Ca-Si-H dissolution rates, which decreased the rate of V release by an order of magnitude. Overall, the results indicate that the BOF slag leaching mechanism evolves from a situation initially dominated by rapid hydration and dissolution of primary dicalcium silicate/free-lime phases, to a slow diffusion limited process controlled by the solubility of secondary Ca-Si-H and CaCO3 phases that replace and cover more reactive primary slag phases at particle surfaces.

Sustained Bauxite Residue Rehabilitation with Gypsum and Organic Matter 16 years after Initial Treatment.

Bauxite residue is a high volume byproduct of alumina manufacture which is commonly disposed of in purpose-built bauxite residue disposal areas (BRDAs). Natural waters interacting with bauxite residue are characteristically highly alkaline, and have elevated concentrations of Na, Al, and other trace metals. Rehabilitation of BRDAs is therefore often costly and resource/infrastructure intensive. Data is presented from three neighboring plots of bauxite residue that was deposited 20 years ago. One plot was amended 16 years ago with process sand, organic matter, gypsum, and seeded (fully treated), another plot was amended 16 years ago with process sand, organic matter, and seeded (partially treated), and a third plot was left untreated. These surface treatments lower alkalinity and salinity, and thus produce a substrate more suitable for biological colonisation from seeding. The reduction of pH leads to much lower Al, V, and As mobility in the actively treated residue and the beneficial effects of treatment extend passively 20-30 cm below the depth of the original amendment. These positive rehabilitation effects are maintained after 2 decades due to the presence of an active and resilient biological community. This treatment may provide a lower cost solution to BRDA end of use closure plans and orphaned BRDA rehabilitation.

Mechanism of Vanadium Leaching during Surface Weathering of Basic Oxygen Furnace Steel Slag Blocks: A Microfocus X-ray Absorption Spectroscopy and Electron Microscopy Study.

Basic oxygen furnace (BOF) steelmaking slag is enriched in potentially toxic V which may become mobilized in high pH leachate during weathering. BOF slag was weathered under aerated and air-excluded conditions for 6 months prior to SEM/EDS and µXANES analysis to determine V host phases and speciation in both primary and secondary phases. Leached blocks show development of an altered region in which free lime and dicalcium silicate phases were absent and Ca-Si-H was precipitated (CaCO3 was also present under aerated conditions). µXANES analyses show that V was released to solution as V(V) during dicalcium silicate dissolution and some V was incorporated into neo-formed Ca-Si-H. Higher V concentrations were observed in leachate under aerated conditions than in the air-excluded leaching experiment. Aqueous V concentrations were controlled by Ca3(VO4)2 solubility, which demonstrate an inverse relationship between Ca and V concentrations. Under air-excluded conditions Ca concentrations were controlled by dicalcium silicate dissolution and Ca-Si-H precipitation, leading to relatively high Ca and correspondingly low V concentrations. Formation of CaCO3 under aerated conditions provided a sink for aqueous Ca, allowing higher V concentrations limited by kinetic dissolution rates of dicalcium silicate. Thus, V release may be slowed by the precipitation of secondary phases in the altered region, improving the prospects for slag reuse.

The fission yeast MTREC and EJC orthologs ensure the maturation of meiotic transcripts during meiosis.

Meiosis is a highly regulated process by which genetic information is transmitted through sexual reproduction. It encompasses unique mechanisms that do not occur in vegetative cells, producing a distinct, well-regulated meiotic transcriptome. During vegetative growth, many meiotic genes are constitutively transcribed, but most of the resulting mRNAs are rapidly eliminated by the Mmi1-MTREC (Mtl1-Red1 core) complex. While Mmi1-MTREC targets premature meiotic RNAs for degradation by the nuclear 3'-5' exoribonuclease exosome during mitotic growth, its role in meiotic gene expression during meiosis is not known. Here, we report that Red5, an essential MTREC component, interacts with pFal1, an ortholog of eukaryotic translation initiation factor eIF4aIII in the fission yeast Schizosaccharomyces pombe In mammals, together with MAGO (Mnh1), Rnps1, and Y14, elF4AIII (pFal1) forms the core of the exon junction complex (EJC), which is essential for transcriptional surveillance and localization of mature mRNAs. In fission yeast, two EJC orthologs, pFal1 and Mnh1, are functionally connected with MTREC, specifically in the process of meiotic gene expression during meiosis. Although pFal1 interacts with Mnh1, Y14, and Rnps1, its association with Mnh1 is not disrupted upon loss of Y14 or Rnps1. Mutations of Red1, Red5, pFal1, or Mnh1 produce severe meiotic defects; the abundance of meiotic transcripts during meiosis decreases; and mRNA maturation processes such as splicing are impaired. Since studying meiosis in mammalian germline cells is difficult, our findings in fission yeast may help to define the general mechanisms involved in accurate meiotic gene expression in higher eukaryotes.

Structural Fe(II) Oxidation in Biotite by an Ectomycorrhizal Fungi Drives Mechanical Forcing.

Microorganisms are essential agents of Earth's soil weathering engine who help transform primary rock-forming minerals into soils. Mycorrhizal fungi, with their vast filamentous networks in symbiosis with the roots of most plants can alter a large number of minerals via local acidification, targeted excretion of ligands, submicron-scale biomechanical forcing, and mobilization of Mg, Fe, Al, and K at the hypha-biotite interface. Here, we present experimental evidence that Paxillus involutus-a basidiomycete fungus-in ectomycorrhizal symbiosis with Scots pine (Pinus sylvestris), is able to oxidize a substantial amount of structural Fe(II) in biotite. Iron redox chemistry, quantified by X-ray absorption near edge spectra on 13 fungi-biotite sections along three distinct hypha colonizing the [001] basal plane of biotite, revealed variable but extensive Fe(II) oxidation up to ∼2 µm in depth and a Fe(III)/Fetotal ratio of up to ∼0.8. The growth of Fe(III) hydroxide implies a volumetric change and a strain within the biotite lattice potentially large enough to induce microcrack formation, which are abundant below the hypha-biotite interface. This Fe(II) oxidation also leads to the formation of a large pool of Fe(III) (i.e., structural Fe(III) and Fe(III) oxyhydroxides) within biotite that could participate in the Fe redox cycling in soils.

Accurate measurements of the Raman scattering coefficient and the depolarization ratio in liquid water.

Despite a long history, the Raman scattering coefficient of water has so far only been measured with 10% uncertainty using a 95% confidence interval. In this paper, we present an experiment where we have achieved 1.5% uncertainty by using a low concentration of Rhodamine 6G in ethanol as a reference along with accurate consideration of polarization-related effects and the geometry of the experimental setup. We have found that the photon-to-photon Raman scattering coefficient of the OH stretching band of liquid water is (1.84±0.03)×10(-4) m(-1) when integrated over the spectral frequency range from 620 to 700 nm while the exciting laser operates at 532 nm. We have also accurately measured the depolarization ratio across this band.

Statistical evaluation of data from multi-laboratory testing of a measurement method intended to indicate the presence of dust resulting from the collapse of the World Trade Center.

In this paper we describe a statistical analysis of the inter-laboratory data summarized in Rosati et al. (2008) to assess the performance of an analytical method to detect the presence of dust from the collapse of the World Trade Center (WTC) on September 11, 2001. The focus of the inter-lab study was the measurement of the concentration of slag wool fibers in dust which was considered to be an indicator of WTC dust. Eight labs were provided with two blinded samples each of three batches of dust that varied in slag wool concentration. Analysis of the data revealed that three of labs, which did not meet measurement quality objectives set forth prior to the experimental work, were statistically distinguishable from the five labs that did meet the quality objectives. The five labs, as a group, demonstrated better measurement capability although their ability to distinguish between the batches was somewhat mixed. This work provides important insights for the planning and implementation of future studies involving examination of dust samples for physical contaminants. This work demonstrates (a) the importance of controlling the amount of dust analyzed, (b) the need to take additional replicates to improve count estimates, and (c) the need to address issues related to the execution of the analytical methodology to ensure all labs meet the measurement quality objectives.

Battery power comparison to charge medical devices in developing countries.

Many people in developing countries cannot afford or rely on certain modes of electricity. We establish the reasonability of relying on lead-acid batteries, 9 V alkaline batteries, and lithium-ion batteries for charging low-voltage medical equipment. Based on the research and tests we conducted, we determined that using these battery types to charge medical devices truly is a reasonable solution.

Efficient methodology for the cyclization of linear peptide libraries via intramolecular S-alkylation using Multipin solid phase peptide synthesis.

Methodology is described here for the efficient parallel synthesis and cyclization of linear peptide libraries using intramolecular S-alkylation chemistry in combination with Multipin solid phase peptide synthesis (Multipin SPPS). The effective use of this methodology was demonstrated with the synthesis of a 72-member combinatorial library of cyclic thioether peptide derivatives of the conserved four-residue structural motif DD/EXK found in the active sites of the five crystallographically defined orthodox type II restriction endonucleases, EcoRV, EcoRI, PvuII, BamHI and BglI.