Autoimmune Hemolytic Anemia (AIHA) Secondary to Cytomegalovirus (CMV) Infection in a 2-Month-Old Infant: A Case Report.

Autoimmune hemolytic anemia (AIHA) is a rare hematologic disorder in the pediatric population and most cases are associated with microbiological infection. The pathological process is not completely clear, but some evidence suggests immunological dysregulation triggered by bacterial or viral infections. Based on the thermal range of the pathogenic antibody, AIHA can be divided into warm (WAIHA) and cold (CAIHA) groups. Cytomegalovirus (CMV) is one of the most common viruses reported as a trigger of AIHA. We present an unusual case of AIHA in a 2-month-old infant positive for both the direct antiglobulin test (C3 complement fraction) and CMV-Polymerase chain reaction in blood samples. In this case, the dating of the infection was uncertain, making it impossible to discriminate between congenital flare-up or a primary acute episode, emphasizing the importance of CMV prenatal testing as a screening measure. We adopted multiple therapeutic strategies including steroids (methylprednisolone and prednisone), Intravenous Immunoglobulin, antivirals (ganciclovir and valganciclovir), and red blood cell transfusion.

Fecal microbiota transfer between young and aged mice reverses hallmarks of the aging gut, eye, and brain.

BACKGROUND: Altered intestinal microbiota composition in later life is associated with inflammaging, declining tissue function, and increased susceptibility to age-associated chronic diseases, including neurodegenerative dementias. Here, we tested the hypothesis that manipulating the intestinal microbiota influences the development of major comorbidities associated with aging and, in particular, inflammation affecting the brain and retina. METHODS: Using fecal microbiota transplantation, we exchanged the intestinal microbiota of young (3 months), old (18 months), and aged (24 months) mice. Whole metagenomic shotgun sequencing and metabolomics were used to develop a custom analysis workflow, to analyze the changes in gut microbiota composition and metabolic potential. Effects of age and microbiota transfer on the gut barrier, retina, and brain were assessed using protein assays, immunohistology, and behavioral testing. RESULTS: We show that microbiota composition profiles and key species enriched in young or aged mice are successfully transferred by FMT between young and aged mice and that FMT modulates resulting metabolic pathway profiles. The transfer of aged donor microbiota into young mice accelerates age-associated central nervous system (CNS) inflammation, retinal inflammation, and cytokine signaling and promotes loss of key functional protein in the eye, effects which are coincident with increased intestinal barrier permeability. Conversely, these detrimental effects can be reversed by the transfer of young donor microbiota. CONCLUSIONS: These findings demonstrate that the aging gut microbiota drives detrimental changes in the gut-brain and gut-retina axes suggesting that microbial modulation may be of therapeutic benefit in preventing inflammation-related tissue decline in later life. Video abstract.

An optimised protocol for detection of SARS-CoV-2 in stool.

BACKGROUND: SARS-CoV-2 has been detected in stool samples of COVID-19 patients, with potential implications for faecal-oral transmission. Compared to nasopharyngeal swab samples, the complexity of the stool matrix poses a challenge in the detection of the virus that has not yet been solved. However, robust and reliable methods are needed to estimate the prevalence and persistence of SARS-CoV-2 in the gut and to ensure the safety of microbiome-based procedures such as faecal microbiota transplant (FMT). The aim of this study was to establish a sensitive and reliable method for detecting SARS-CoV-2 in stool samples. RESULTS: Stool samples from individuals free of SARS-CoV-2 were homogenised in saline buffer and spiked with a known titre of inactivated virus ranging from 50 to 750 viral particles per 100 mg stool. Viral particles were concentrated by ultrafiltration, RNA was extracted, and SARS-CoV-2 was detected via real-time reverse-transcription polymerase chain reaction (RT-qPCR) using the CDC primers and probes. The RNA extraction procedure we used allowed for the detection of SARS-CoV-2 via RT-qPCR in most of the stool samples tested. We could detect as few as 50 viral particles per 100 mg of stool. However, high variability was observed across samples at low viral titres. The primer set targeting the N1 region provided more reliable and precise results and for this primer set our method had a limit of detection of 1 viral particle per mg of stool. CONCLUSIONS: Here we describe a sensitive method for detecting SARS-CoV-2 in stool samples. This method can be used to establish the persistence of SARS-CoV-2 in stool and ensure the safety of clinical practices such as FMT.

Hypophosphataemia is common in patients with aneurysmal subarachnoid haemorrhage.

INTRODUCTION: Hypophosphataemia is common in critically ill patients, but neither its prevalence nor its association with outcome have been investigated specifically in patients with aneurysmal subarachnoid haemorrhage (aSAH). METHODS: Patients with aSAH and at least one phosphate measurement were included from two independent cohorts; an American cohort extracted from two open-access databases (Medical Information Mart for Intensive Care-III and eICU Collaborative Research Database v. 2.0) and a Danish cohort consisting of patients with aSAH admitted to Rigshospitalet, Denmark over a 4-year period. In each cohort, we calculated the prevalence of mild (0.32-0.80 mmol/L) and severe (<0.32 mmol/L) hypophosphataemia and their association with in-hospital mortality before and after propensity-score matching. RESULTS: Hypophosphataemia occurred in 72.4% (95% CI: 68.1-76.3) of patients in the American cohort (n = 471) and 54.9% (50.0-59.7) in the Danish cohort (n = 419). However, it was not associated with mortality in neither full (American: Mild, Odds ratio (OR) 0.99 (0.91-1.07), Severe OR 1.20 (0.95-1.51); Danish: Mild, OR 1.01 (0.95-1.08), Severe OR 1.20 (0.95-1.51)) nor propensity-score matched cohorts (American (n = 168): Mild, OR 1.06 (0.88-1.28), Severe OR 1.46 (0.96-2.12); Danish (n = 44): Mild, OR 1.16 (0.82-1.65), Severe OR 0.45 (0.13-1.55)). CONCLUSION: In this retrospective study of patients with aSAH, hypophosphataemia was common.

Insights into the Cultured Bacterial Fraction of Corals.

Bacteria associated with coral hosts are diverse and abundant, with recent studies suggesting involvement of these symbionts in host resilience to anthropogenic stress. Despite their putative importance, the work dedicated to culturing coral-associated bacteria has received little attention. Combining published and unpublished data, here we report a comprehensive overview of the diversity and function of culturable bacteria isolated from corals originating from tropical, temperate, and cold-water habitats. A total of 3,055 isolates from 52 studies were considered by our metasurvey. Of these, 1,045 had full-length 16S rRNA gene sequences, spanning 138 formally described and 12 putatively novel bacterial genera across the Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria phyla. We performed comparative genomic analysis using the available genomes of 74 strains and identified potential signatures of beneficial bacterium-coral symbioses among the strains. Our analysis revealed >400 biosynthetic gene clusters that underlie the biosynthesis of antioxidant, antimicrobial, cytotoxic, and other secondary metabolites. Moreover, we uncovered genomic features-not previously described for coral-bacterium symbioses-potentially involved in host colonization and host-symbiont recognition, antiviral defense mechanisms, and/or integrated metabolic interactions, which we suggest as novel targets for the screening of coral probiotics. Our results highlight the importance of bacterial cultures to elucidate coral holobiont functioning and guide the selection of probiotic candidates to promote coral resilience and improve holistic and customized reef restoration and rehabilitation efforts. IMPORTANCE Our paper is the first study to synthesize currently available but decentralized data of cultured microbes associated with corals. We were able to collate 3,055 isolates across a number of published studies and unpublished collections from various laboratories and researchers around the world. This equated to 1,045 individual isolates which had full-length 16S rRNA gene sequences, after filtering of the original 3,055. We also explored which of these had genomes available. Originally, only 36 were available, and as part of this study, we added a further 38-equating to 74 in total. From this, we investigated potential genetic signatures that may facilitate a host-associated lifestyle. Further, such a resource is an important step in the selection of probiotic candidates, which are being investigated for promoting coral resilience and potentially applied as a novel strategy in reef restoration and rehabilitation efforts. In the spirit of open access, we have ensured this collection is available to the wider research community through the web site http://isolates.reefgenomics.org/ with the hope many scientists across the globe will ask for access to these cultures for future studies.

Meta-analysis of the Parkinson's disease gut microbiome suggests alterations linked to intestinal inflammation.

The gut microbiota is emerging as an important modulator of neurodegenerative diseases, and accumulating evidence has linked gut microbes to Parkinson's disease (PD) symptomatology and pathophysiology. PD is often preceded by gastrointestinal symptoms and alterations of the enteric nervous system accompany the disease. Several studies have analyzed the gut microbiome in PD, but a consensus on the features of the PD-specific microbiota is missing. Here, we conduct a meta-analysis re-analyzing the ten currently available 16S microbiome datasets to investigate whether common alterations in the gut microbiota of PD patients exist across cohorts. We found significant alterations in the PD-associated microbiome, which are robust to study-specific technical heterogeneities, although differences in microbiome structure between PD and controls are small. Enrichment of the genera Lactobacillus, Akkermansia, and Bifidobacterium and depletion of bacteria belonging to the Lachnospiraceae family and the Faecalibacterium genus, both important short-chain fatty acids producers, emerged as the most consistent PD gut microbiome alterations. This dysbiosis might result in a pro-inflammatory status which could be linked to the recurrent gastrointestinal symptoms affecting PD patients.

Association Between ICU-Acquired Hypernatremia and In-Hospital Mortality: Data From the Medical Information Mart for Intensive Care III and the Electronic ICU Collaborative Research Database.

OBJECTIVES: Describe the relationship between ICU-acquired hypernatremia and in-hospital mortality and investigate the optimal hypernatremia correction rate. DESIGN SETTING PARTICIPANTS AND MEASUREMENTS: Observational study including two individual ICU cohorts. We used the Medical Information Mart for Intensive Care III v. 1.4 database consists of all ICU patients admitted to the Beth Israel Deaconess Medical Center in Boston from 2001 to 2012 (n = 46,476). The electronic ICU v. 2.0 database consists of all ICU patients admitted to 208 distinct hospitals across the United States from 2014 to 2015 (n = 200,859). We included all adult patients admitted to an ICU with two consecutive sodium samples within normal range (135-145 mmol/L) and without two consecutive hyponatremic samples (< 135 mmol/L) during the ICU stay. RESULTS: Of 23,445 patients identified in Medical Information Mart for Intensive Care III, 9% (n = 2,172) developed hypernatremia during their ICU stay. In electronic ICU, 88,160 patients were identified and 7% (n = 5,790) developed hypernatremia. In both cohorts, patients with hypernatremia had a higher mortality (Medical Information Mart for Intensive Care III: 20% vs 42%; p < 0.01 and electronic ICU: 6% vs 22%; p < 0.01), with hypernatremia increasing the risk of in-hospital mortality (Medical Information Mart for Intensive Care III: odds ratio, 1.15; 95% CI, 1.13-1.17 and electronic ICU: odds ratio, 1.11; 95% CI, 1.10-1.12) and over time using a Cox regression. Rapid sodium correction rate (> 0.5 mmol/L/hr) was associated with an increased in-hospital mortality in both cohorts (Medical Information Mart for Intensive Care III: odds ratio, 1.08; 95% CI, 1.03-1.13 and electronic ICU: odds ratio, 1.10; 95% CI, 1.06-1.13). In the electronic ICU cohort, rapid correction rates were associated with a significant difference in in-hospital mortality, but there was no statistically significant association in the Medical Information Mart for Intensive Care III cohort. CONCLUSIONS: ICU-acquired hypernatremia is associated with increased in-hospital mortality. Furthermore, a rapid sodium correction rates may be harmful. This suggests it is important to both prevent ICU-acquired hypernatremia and to avoid rapid correction rates if a patient becomes hypernatremic.

Prediction of Septic Shock Onset in ICU by Instantaneous Monitoring of Vital Signs.

Septic Shock is a critical pathological state that affects patients entering the intensive care unit (ICU). Many studies have been directed to characterize and predict the onset of the septic shock, both in ICU and in the Emergency Department employing data extracted from the Electronic Health Records. Recently, machine learning algorithms have been successfully employed to help characterize septic shock in a more objective and automatic fashion. Only a few of these studies employ information contained in the continuously recorded vital signs such as electrocardiogram and arterial blood pressure. In particular, we have devised a novel feature estimation procedure able to consider instantaneous dynamics related to cardiovascular control. This work aims at developing a short-term prediction algorithm for identifying patients experiencing septic shock among a population of 100 septic patients extracted from the MIMIC-III clinical and waveform database. Among all the results obtained from several trained machine learning models, the best performance reached an AUC on the test set equal to 0.93 (Accuracy=0.85, Sensitivity=0.89 and Specificity=0.82).

Microwave based regenerating permeable reactive barriers (MW-PRBs): Proof of concept and application for Cs removal.

The present study evaluates the concept of permeable reactive barrier (PRB) coupled with microwaves (MWs) as in situ-regenerating technology with focus on Cs-contaminated water. Experimental and modelling results data from batch and column tests were carried out, evaluating several chemical-physical and environmental parameters. Main results showed a very rapid increase in GAC temperature during MW irradiation up to ∼680 °C. This highlights the GAC strong ability to transform MW power into heat due to GAC excellent dielectric properties (ε' = 13.8). Physical characterization revealed that GAC pore volume and specific surface area change with the number of regeneration cycles. GAC regeneration efficiency variation reflects this behaviour with a maximum value of ∼112% (5th cycle). The final GAC weight loss of ∼7% further demonstrates GAC life span preservation during MW irradiation. Results from column tests confirms that GAC can be regenerated by MW also in dynamic condition, due to sublimation/vaporization and vapour stripping Cs removal mechanisms and that the regeneration effectiveness is time-dependent. The breakthrough curve shape confirms significant benefits from MW irradiation. Overall, obtained finding demonstrated the feasibility of the proposed concept, also providing essential data to guide its scaling-up application.

Field technical applicability and cost analysis for microwave based regenerating permeable reactive barriers (MW-PRBs) operating in Cs-contaminated groundwater treatment.

The present study tests the potentiality of a novel microwave based regenerating permeable reactive barrier (MW-PRB) system as combined treatment for Cs-contaminated groundwater. Granular activated carbon (GAC) was selected as adsorptive materials in batch and column MW-regeneration experiments. Experimental and modeling data were elaborated for technical and economic considerations in order to assess the MW-PRB feasibility jointly with essential information regarding its real field applicability. Batch experiments investigated the effects of 10 adsorption-MW regeneration cycles under different MW irradiation conditions (applied electric field = 200-460 V m-1; irradiation times = 1-15 min) by assessing GAC variation properties in term of regeneration yield (δ), specific area and weight loss (WL) variation. Column tests were carried using a dedicated setup essentially including a column filled with GAC implanted in a MW oven cavity (MW electric field of 385 V m-1, irradiation times 5-15 min). Lab-scale results shown the ability of MW in Cs removal from GAC as demonstrated by regeneration yield (δ = 79-110%) and WL (6.78% for 10 cycles) values. This was confirmed in dynamic conditions by data from MW-column tests highlighting the highest Cs removal of ~80% when the maximum regeneration time was applied. Residual Cs concentration in breakthrough curves fitted well with the proposed Yoon and Nelson model (R2 = ~0.97). Results from techno-economic analysis revealed the MW-PRB viability and its advantages also in comparison with conventional PRB systems, demonstrating the concept of combined MW-PRB treatment. Saved cost obtained demonstrated in fact the potential cost effectiveness of MW-PRB system and, consequently, the implementation of novel approach is encouraged. Calculated PRB longevity vs groundwater velocity curves are useful in order to predict long-term PRB performance and the response of the remediation activities, as well as for guiding the design and the scaling-up of MW-PRB treatment.

Functional diversity enables multiple symbiont strains to coexist in deep-sea mussels.

Genetic diversity of closely related free-living microorganisms is widespread and underpins ecosystem functioning, but most evolutionary theories predict that it destabilizes intimate mutualisms. Accordingly, strain diversity is assumed to be highly restricted in intracellular bacteria associated with animals. Here, we sequenced metagenomes and metatranscriptomes of 18 Bathymodiolus mussel individuals from four species, covering their known distribution range at deep-sea hydrothermal vents in the Atlantic. We show that as many as 16 strains of intracellular, sulfur-oxidizing symbionts coexist in individual Bathymodiolus mussels. Co-occurring symbiont strains differed extensively in key functions, such as the use of energy and nutrient sources, electron acceptors and viral defence mechanisms. Most strain-specific genes were expressed, highlighting their potential to affect fitness. We show that fine-scale diversity is pervasive in Bathymodiolus sulfur-oxidizing symbionts, and hypothesize that it may be widespread in low-cost symbioses where the environment, rather than the host, feeds the symbionts.

Scientific communication strategies of microbiologists in the era of social media.

Over the last decades, the world of communication underwent drastic changes, and internet and social media emerged as essential vehicles for exchanging information. Following these trends, it is important that scientists adapt to changes and adopt optimal strategies to communicate with colleagues, lay people and institutions. We conducted an online survey to investigate the communication strategies of microbiologists and their colleagues from other disciplines. We collected data from 527 scholars from 57 countries, with ∼42% of them being microbiologists. We focused particularly on social media and found that >80% of participants used them for work, and that ∼50% of interviewed actively shared and gathered scientific contents from social media. Compared to colleagues from other fields, microbiologists were less averse to use social media for work and were also less accustomed to use pre-prints as a source and vehicle of information. However, a large proportion of microbiologists declared to have planned pre-print publications in the future. Surprisingly, our data revealed that age is a poor predictor of social media usage, but it is strongly associated with the type of social media used, the activity undertaken on them and the attitude towards pre-print publications. Considering the kaleidoscopic variety of scientific communication tools, our data might help to optimize the scientific promotion strategies among microbiologists.

Extending the "One Strain Many Compounds" (OSMAC) Principle to Marine Microorganisms.

Genomic data often highlights an inconsistency between the number of gene clusters identified using bioinformatic approaches as potentially producing secondary metabolites and the actual number of chemically characterized secondary metabolites produced by any given microorganism. Such gene clusters are generally considered as "silent", meaning that they are not expressed under laboratory conditions. Triggering expression of these "silent" clusters could result in unlocking the chemical diversity they control, allowing the discovery of novel molecules of both medical and biotechnological interest. Therefore, both genetic and cultivation-based techniques have been developed aimed at stimulating expression of these "silent" genes. The principles behind the cultivation based approaches have been conceptualized in the "one strain many compounds" (OSMAC) framework, which underlines how a single strain can produce different molecules when grown under different environmental conditions. Parameters such as, nutrient content, temperature, and rate of aeration can be easily changed, altering the global physiology of a microbial strain and in turn significantly affecting its secondary metabolism. As a direct extension of such approaches, co-cultivation strategies and the addition of chemical elicitors have also been used as cues to activate "silent" clusters. In this review, we aim to provide a focused and comprehensive overview of these strategies as they pertain to marine microbes. Moreover, we underline how changes in some parameters which have provided important results in terrestrial microbes, but which have rarely been considered in marine microorganisms, may represent additional strategies to awaken "silent" gene clusters in marine microbes. Unfortunately, the empirical nature of the OSMAC approach forces scientists to perform extensive laboratory experiments. Nevertheless, we believe that some computation and experimental based techniques which are used in other disciplines, and which we discuss; could be effectively employed to help streamline the OSMAC based approaches. We believe that natural products discovery in marine microorganisms would be greatly aided through the integration of basic microbiological approaches, computational methods, and technological innovations, thereby helping unearth much of the as yet untapped potential of these microorganisms.

Characterization of the First "Candidatus Nitrotoga" Isolate Reveals Metabolic Versatility and Separate Evolution of Widespread Nitrite-Oxidizing Bacteria.

Nitrification is a key process of the biogeochemical nitrogen cycle and of biological wastewater treatment. The second step, nitrite oxidation to nitrate, is catalyzed by phylogenetically diverse, chemolithoautotrophic nitrite-oxidizing bacteria (NOB). Uncultured NOB from the genus "Candidatus Nitrotoga" are widespread in natural and engineered ecosystems. Knowledge about their biology is sparse, because no genomic information and no pure "Ca Nitrotoga" culture was available. Here we obtained the first "Ca Nitrotoga" isolate from activated sludge. This organism, "Candidatus Nitrotoga fabula," prefers higher temperatures (>20°C; optimum, 24 to 28°C) than previous "Ca Nitrotoga" enrichments, which were described as cold-adapted NOB. "Ca Nitrotoga fabula" also showed an unusually high tolerance to nitrite (activity at 30 mM NO2-) and nitrate (up to 25 mM NO3-). Nitrite oxidation followed Michaelis-Menten kinetics, with an apparent Km (Km(app)) of ~89 µM nitrite and a Vmax of ~28 µmol of nitrite per mg of protein per h. Key metabolic pathways of "Ca Nitrotoga fabula" were reconstructed from the closed genome. "Ca Nitrotoga fabula" possesses a new type of periplasmic nitrite oxidoreductase belonging to a lineage of mostly uncharacterized proteins. This novel enzyme indicates (i) separate evolution of nitrite oxidation in "Ca Nitrotoga" and other NOB, (ii) the possible existence of phylogenetically diverse, unrecognized NOB, and (iii) together with new metagenomic data, the potential existence of nitrite-oxidizing archaea. For carbon fixation, "Ca Nitrotoga fabula" uses the Calvin-Benson-Bassham cycle. It also carries genes encoding complete pathways for hydrogen and sulfite oxidation, suggesting that alternative energy metabolisms enable "Ca Nitrotoga fabula" to survive nitrite depletion and colonize new niches.IMPORTANCE Nitrite-oxidizing bacteria (NOB) are major players in the biogeochemical nitrogen cycle and critical for wastewater treatment. However, most NOB remain uncultured, and their biology is poorly understood. Here, we obtained the first isolate from the environmentally widespread NOB genus "Candidatus Nitrotoga" and performed a detailed physiological and genomic characterization of this organism ("Candidatus Nitrotoga fabula"). Differences between key phenotypic properties of "Ca Nitrotoga fabula" and those of previously enriched "Ca Nitrotoga" members reveal an unexpectedly broad range of physiological adaptations in this genus. Moreover, genes encoding components of energy metabolisms outside nitrification suggest that "Ca Nitrotoga" are ecologically more flexible than previously anticipated. The identification of a novel nitrite-oxidizing enzyme in "Ca Nitrotoga fabula" expands our picture of the evolutionary history of nitrification and might lead to discoveries of novel nitrite oxidizers. Altogether, this study provides urgently needed insights into the biology of understudied but environmentally and biotechnologically important microorganisms.

Ecology and Biotechnological Potential of Bacteria Belonging to the Genus Pseudovibrio.

Members of the genus Pseudovibrio have been isolated worldwide from a great variety of marine sources as both free-living and host-associated bacteria. So far, the available data depict a group of alphaproteobacteria characterized by a versatile metabolism, which allows them to use a variety of substrates to meet their carbon, nitrogen, sulfur, and phosphorous requirements. Additionally, Pseudovibrio-related bacteria have been shown to proliferate under extreme oligotrophic conditions, tolerate high heavy-metal concentrations, and metabolize potentially toxic compounds. Considering this versatility, it is not surprising that they have been detected from temperate to tropical regions and are often the most abundant isolates obtained from marine invertebrates. Such an association is particularly recurrent with marine sponges and corals, animals that play a key role in benthic marine systems. The data so far available indicate that these bacteria are mainly beneficial to the host, and besides being involved in major nutrient cycles, they could provide the host with both vitamins/cofactors and protection from potential pathogens via the synthesis of antimicrobial secondary metabolites. In fact, the biosynthetic abilities of Pseudovibrio spp. have been emerging in recent years, and both genomic and analytic studies have underlined how these organisms promise novel natural products of biotechnological value.

Identification of Secondary Metabolite Gene Clusters in the Pseudovibrio Genus Reveals Encouraging Biosynthetic Potential toward the Production of Novel Bioactive Compounds.

Increased incidences of antimicrobial resistance and the emergence of pan-resistant 'superbugs' have provoked an extreme sense of urgency amongst researchers focusing on the discovery of potentially novel antimicrobial compounds. A strategic shift in focus from the terrestrial to the marine environment has resulted in the discovery of a wide variety of structurally and functionally diverse bioactive compounds from numerous marine sources, including sponges. Bacteria found in close association with sponges and other marine invertebrates have recently gained much attention as potential sources of many of these novel bioactive compounds. Members of the genus Pseudovibrio are one such group of organisms. In this study, we interrogate the genomes of 21 Pseudovibrio strains isolated from a variety of marine sources, for the presence, diversity and distribution of biosynthetic gene clusters (BGCs). We expand on results obtained from antiSMASH analysis to demonstrate the similarity between the Pseudovibrio-related BGCs and those characterized in other bacteria and corroborate our findings with phylogenetic analysis. We assess how domain organization of the most abundant type of BGCs present among the isolates (Non-ribosomal peptide synthetases and Polyketide synthases) may influence the diversity of compounds produced by these organisms and highlight for the first time the potential for novel compound production from this genus of bacteria, using a genome guided approach.

Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle.

Nitrification, the oxidation of ammonia (NH3) via nitrite (NO2-) to nitrate (NO3-), is a key process of the biogeochemical nitrogen cycle. For decades, ammonia and nitrite oxidation were thought to be separately catalysed by ammonia-oxidizing bacteria (AOB) and archaea (AOA), and by nitrite-oxidizing bacteria (NOB). The recent discovery of complete ammonia oxidizers (comammox) in the NOB genus Nitrospira, which alone convert ammonia to nitrate, raised questions about the ecological niches in which comammox Nitrospira successfully compete with canonical nitrifiers. Here we isolate a pure culture of a comammox bacterium, Nitrospira inopinata, and show that it is adapted to slow growth in oligotrophic and dynamic habitats on the basis of a high affinity for ammonia, low maximum rate of ammonia oxidation, high growth yield compared to canonical nitrifiers, and genomic potential for alternative metabolisms. The nitrification kinetics of four AOA from soil and hot springs were determined for comparison. Their surprisingly poor substrate affinities and lower growth yields reveal that, in contrast to earlier assumptions, AOA are not necessarily the most competitive ammonia oxidizers present in strongly oligotrophic environments and that N. inopinata has the highest substrate affinity of all analysed ammonia oxidizer isolates except the marine AOA Nitrosopumilus maritimus SCM1 (ref. 3). These results suggest a role for comammox organisms in nitrification under oligotrophic and dynamic conditions.

Application of a γRS index-based method and techno-economic analysis for in situ treatment of 137Cs-contaminated soils by cement-barite based stabilisation/solidification.

This paper examines the application of cement (C)-barite (Ba) based-Stabilisation/Solidification (S/S) for the remediation of 137Cs-contaminated soils, investigating the influence of soil: grout and C: Ba ratios on the shielding performance of the S/S mix assessed as gamma radiation shielding (γRS) index variation. Results from experiments were used to perform a novel approach and an economic analysis in order to calculate the effective dose reduction achievable by S/S and to assess the optimum quantities and costs of selected mixes, respectively. Gamma ray spectrometer measurements indicate that γRS index increases with increasing barite percentage up to a maximum level of 50%; however a further increase results in a worsening of the shielding performances. A maximum γRS variation of 46.5% was recorded with grout percentage increasing from 16.6 to 50%. At the photon energy of 662 keV (137Cs), the maximum grout amount results in the possibility to shield up to 24.1% of γ-rays emitted. The effective dose reduction achievable by the investigated S/S allows a maximum 137Cs-soil contamination in the range 2.94-14.55 kBq kg-1 successfully treatable employing a soil: grout ratio of 1: 1 (C: Ba = 1:1). Technical data, jointly with economic analysis findings, make cement-barite based-S/S very competitive in cost-effectiveness and could provide a basis for decision-making of 137Cs-contaminated site remediation.

Phosphate Limitation Triggers the Dissolution of Precipitated Iron by the Marine Bacterium Pseudovibrio sp. FO-BEG1.

Phosphorus is an essential nutrient for all living organisms. In bacteria, the preferential phosphorus source is phosphate, which is often a limiting macronutrient in many areas of the ocean. The geochemical cycle of phosphorus is strongly interconnected with the cycles of other elements and especially iron, because phosphate tends to adsorb onto iron minerals, such as iron oxide formed in oxic marine environments. Although the response to either iron or phosphate limitation has been investigated in several bacterial species, the metabolic interplay between these two nutrients has rarely been considered. In this study we evaluated the impact of phosphate limitation on the iron metabolism of the marine bacterium Pseudovibrio sp. FO-BEG1. We observed that phosphate limitation led to an initial decrease of soluble iron in the culture up to three times higher than under phosphate surplus conditions. Similarly, a decrease in soluble cobalt was more pronounced under phosphate limitation. These data point toward physiological changes induced by phosphate limitation that affect either the cellular surface and therefore the metal adsorption onto it or the cellular metal uptake. We discovered that under phosphate limitation strain FO-BEG1, as well as selected strains of the Roseobacter clade, secreted iron-chelating molecules. This leads to the hypothesis that these bacteria might release such molecules to dissolve iron minerals, such as iron-oxyhydroxide, in order to access the adsorbed phosphate. As the adsorption of phosphate onto iron minerals can significantly decrease phosphate concentrations in the environment, the observed release of iron-chelators might represent an as yet unrecognized link between the biogeochemical cycle of phosphorus and iron, and it suggests another biological function of iron-chelating molecules in addition to metal-scavenging.

Stabilisation/solidification of 137Cs-contaminated soils using novel high-density grouts: γ-ray shielding properties, contaminant immobilisation and a γRS index-based approach for in situ applicability.

In this work, γ-ray shielding and Cs immobilisation performances of high-density magnetite (MG) and iron powder (IP) in Portland cement (PC) based-S/S treatment were investigated. Experimental results were elaborated using a γ-radiation shielding (γRS) index-based approach for assessing the effectiveness of in situ S/S of 137Cs-contaminated soils. Main results reveal that the replacement of PC by MG or IP (up to 50%) leads to a marked increase (up to about 4-fold) in the γ-ray shielding performance, whereas a further material addition decreases the S/S shielding performance. The highest γRS index of ∼26% (662 keV) was found in the case of IP addition (33.3%). The use of MG-mixes allows reaching slightly slower γRS index jointly with the highest Cs-immobilisation of 97.8%. In this case, calculation shows a maximum 137Cs-contamination level successfully treatable by in situ S/S up to ∼2.9 or ∼14.5 kBq kg-1 for the realistic or low probability scenario, respectively, highlighting the possibility to remediate a very wide range of real contamination. Findings show MG - PC S/S as the best choice and could provide a basis for decision-making of S/S remediation of 137Cs-contaminated sites.