Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface

Contains fulltext : 205810pub.pdf (publisher's version ) (Open Access)Summary The recently discovered comammox process encompasses both nitrification steps, the aerobic oxidation of ammonia and nitrite, in a single organism. All known comammox bacteria are affiliated with Nitrospira sublineage II and can be grouped into two distinct clades, referred to as A and B, based on ammonia monooxygenase phylogeny. In this study, we report high-quality draft genomes of two novel comammox Nitrospira from the terrestrial subsurface, representing one clade A and one clade B comammox organism. The two metagenome-assembled genomes were compared with other representatives of Nitrospira sublineage II, including both canonical and comammox Nitrospira. Phylogenomic analyses confirmed the affiliation of the two novel Nitrospira with comammox clades A and B respectively. Based on phylogenetic distance and pairwise average nucleotide identity values, both comammox Nitrospira were classified as novel species. Genomic comparison revealed high conservation of key metabolic features in sublineage II Nitrospira, including respiratory complexes I?V and the machineries for nitrite oxidation and carbon fixation via the reductive tricarboxylic acid cycle. In addition, the presence of the enzymatic repertoire for formate and hydrogen oxidation in the Rifle clades A and B comammox genomes, respectively, suggest a broader distribution of these metabolic features than previously anticipated.11 p

A human monoclonal antibody that specifically binds and inhibits the staphylococcal complement inhibitor protein SCIN

Staphylococcus aureus is a serious public health burden causing a wide variety of infections. Earlier detection of such infections could result in faster and more directed therapies that also prevent resistance development. Human monoclonal antibodies (humAbs) are promising tools for diagnosis and therapy owing to their relatively straightforward synthesis, long history of safe clinical use and high target specificity. Here we show that the humAb 6D4, which was obtained from a random screen of B-cells producing antibodies that bind to whole cells of S. aureus, targets the staphylococcal complement inhibitor (SCIN). The epitope recognized by 6D4 was localized to residues 26 to 36 in the N-terminus of SCIN, which overlap with the active site. Accordingly, 6D4 can inhibit SCIN activity as demonstrated through the analysis of C3b deposition on S. aureus cells and complement-induced lysis of rabbit erythrocytes. Importantly, while SCIN is generally regarded as a secreted virulence factor, 6D4 allowed detection of strongly increased SCIN binding to S. aureus cells upon exposure to human serum, relating to the known binding of SCIN to C3 convertases deposited on the staphylococcal cell surface. Lastly, we show that labeling of humAb 6D4 with a near-infrared fluorophore allows one-step detection of SCIN-producing S. aureus cells. Together, our findings show that the newly described humAb 6D4 specifically recognizes S. aureus SCIN, which can potentially be used for detection of human serum-incubated S. aureus strains expressing SCIN

The RMS Survey: Mid-Infrared Observations of Candidate Massive YSOs in the Southern Hemisphere

Abridged abstract: The Red MSX Source (RMS) survey is an ongoing effort to return a large, well-selected sample of massive young stellar objects (MYSOs) within our Galaxy. A series of ground-based follow-up observations are being undertaken in order to remove contaminant objects from our list of 2000 candidates, and to begin characterising these MYSOs. As a part of these follow-up observations, high resolution (~1") mid-IR imaging aids the identification of contaminant objects which are resolved (UCHII regions, PN) as opposed to those which are unresolved (YSOs, evolved stars) as well as identifying YSOs near UCHII regions and other multiple sources. We present 10.4 micron imaging observations for 346 candidate MYSOs in the RMS survey in the Southern Hemisphere, primarily outside the region covered by the GLIMPSE Spitzer Legacy Survey. These were obtained using TIMMI2 on the ESO 3.6m telescope in La Silla, Chile. Our photometric accuracy is of order 0.05Jy, and our astrometric accuracy is 0.8", which is an improvement over the nominal 2" accuracy of the MSX PSC.Comment: 9 page paper accepted to A&A. Online data for table 2 and figure 1 will be available in the published online version of this paper via A&A. The paper contains 7 figures and 3 table

Complete Genome Sequence of the Aerobic Facultative Methanotroph Methylocella tundrae Strain T4

Methylocella tundrae T4T is a facultative aerobic methanotroph which was isolated from an acidic tundra wetland and possesses only a soluble methane monooxygenase. The complete genome, which includes two megaplasmids, was sequenced using a combination of Illumina and Nanopore technologies. One of the megaplasmids carries a propane monooxygenase gene cluster

A novel mesocosm set-up reveals strong methane emission reduction in submerged peat moss Sphagnum cuspidatum by tightly associated methanotrophs

Wetlands present the largest natural sources of methane (CH_4) and their potential CH_4 emissions greatly vary due to the activity of CH_4-oxidizing bacteria associated with wetland plant species. In this study, the association of CH_4-oxidizing bacteria with submerged Sphagnum peat mosses was studied, followed by the development of a novel mesocosm set-up. This set-up enabled the precise control of CH_4 input and allowed for monitoring the dissolved CH_4in a Sphagnum moss layer while mimicking natural conditions. Two mesocosm set-ups were used in parallel: one containing a Sphagnum moss layer in peat water, and a control only containing peat water. Moss-associated CH_4 oxidizers in the field could reduce net CH_4 emission up to 93%, and in the mesocosm set-up up to 31%. Furthermore, CH_4 oxidation was only associated with Sphagnum, and did not occur in peat water. Especially methanotrophs containing a soluble methane monooxygenase enzyme were significantly enriched during the 32 day mesocosm incubations. Together these findings showed the new mesocosm setup is very suited to study CH_4 cycling in submerged Sphagnum moss community under controlled conditions. Furthermore, the tight associated between Sphagnum peat mosses and methanotrophs can significantly reduce CH_4 emissions in submerged peatlands

Global nitrogen budgets in cereals: A 50-year assessment for maize, rice, and wheat production systems

Industrially produced N-fertilizer is essential to the production of cereals that supports current and projected human populations. We constructed a top-down global N budget for maize, rice, and wheat for a 50-year period (1961 to 2010). Cereals harvested a total of 1551 Tg of N, of which 48% was supplied through fertilizer-N and 4% came from net soil depletion. An estimated 48% (737 Tg) of crop N, equal to 29, 38, and 25 kg ha−1 yr−1 for maize, rice, and wheat, respectively, is contributed by sources other than fertilizer- or soil-N. Non-symbiotic N2 fixation appears to be the major source of this N, which is 370 Tg or 24% of total N in the crop, corresponding to 13, 22, and 13 kg ha−1 yr−1 for maize, rice, and wheat, respectively. Manure (217 Tg or 14%) and atmospheric deposition (96 Tg or 6%) are the other sources of N. Crop residues and seed contribute marginally. Our scaling-down approach to estimate the contribution of non-symbiotic N2 fixation is robust because it focuses on global quantities of N in sources and sinks that are easier to estimate, in contrast to estimating N losses per se, because losses are highly soil-, climate-, and crop-specific

Higher yields and lower methane emissions with new rice cultivars

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this record.Breeding high-yielding rice cultivars through increasing biomass is a key strategy to meet rising global food demands. Yet, increasing rice growth can stimulate methane (CH4 ) emissions, exacerbating global climate change, as rice cultivation is a major source of this powerful greenhouse gas. Here, we show in a series of experiments that high-yielding rice cultivars actually reduce CH4 emissions from typical paddy soils. Averaged across 33 rice cultivars, a biomass increase of 10% resulted in a 10.3% decrease in CH4 emissions in a soil with a high carbon (C) content. Compared to a low-yielding cultivar, a high-yielding cultivar significantly increased root porosity and the abundance of methane-consuming microorganisms, suggesting that the larger and more porous root systems of high-yielding cultivars facilitated CH4 oxidation by promoting O2 transport to soils. Our results were further supported by a meta-analysis, showing that high-yielding rice cultivars strongly decrease CH4 emissions from paddy soils with high organic C contents. Based on our results, increasing rice biomass by 10% could reduce annual CH4 emissions from Chinese rice agriculture by 7.1%. Our findings suggest that modern rice breeding strategies for high-yielding cultivars can substantially mitigate paddy CH4 emission in China and other rice growing regions.This work was supported by the National Key Research and Development Program China (2016YFD0300903, 2016YFD0300501, and 2015BAC02B02), Special Fund for Agro-scientific Research in the Public Interest (201503122), Central Public interest Scientific Institution Basal Research Fund of Institute of Crop Science, the Innovation Program of CAAS (Y2016PT12, Y2016XT01), and the China Scholarship Council

Quantum Extremism: Effective Potential and Extremal Paths

The reality and convexity of the effective potential in quantum field theories has been studied extensively in the context of Euclidean space-time. It has been shown that canonical and path-integral approaches may yield different results, thus resolving the `convexity problem'. We discuss the transferral of these treatments to Minkowskian space-time, which also necessitates a careful discussion of precisely which field configurations give the dominant contributions to the path integral. In particular, we study the effective potential for the N=1 linear sigma model.Comment: 11 pages, 4 figure

The Path-Integral Approach to the N=2 Linear Sigma Model

In QFT the effective potential is an important tool to study symmetry breaking phenomena. It is known that, in some theories, the canonical approach and the path-integral approach yield different effective potentials. In this paper we investigate this for the Euclidean N=2 linear sigma model. Both the Green's functions and the effective potential will be computed in three different ways. The relative merits of the various approaches are discussed.Comment: 2 figure

Spatial Light Modulators for the Manipulation of Individual Atoms

We propose a novel dipole trapping scheme using spatial light modulators (SLM) for the manipulation of individual atoms. The scheme uses a high numerical aperture microscope to map the intensity distribution of a SLM onto a cloud of cold atoms. The regions of high intensity act as optical dipole force traps. With a SLM fast enough to modify the trapping potential in real time, this technique is well suited for the controlled addressing and manipulation of arbitrarily selected atoms.Comment: 9 pages, 5 figure