Effects of soil amendment on gas depth profiles in soil monoliths using direct mass spectrometric measurement

Prevalence of current patterns and predictive trends of multidrug-resistant Salmonella Typhi in Sudan

Background

Enteric fever has persistence of great impact in Sudanese public health especially during rainy season when the causative agent Salmonella enterica serovar Typhi possesses pan endemic patterns in most regions of Sudan - Khartoum.

Objectives

The present study aims to assess the recent state of antibiotics susceptibility of Salmonella Typhi with special concern to multidrug resistance strains and predict the emergence of new resistant patterns and outbreaks.

Methods

Salmonella Typhi strains were isolated and identified according to the guidelines of the International Standardization Organization and the World Health Organization. The antibiotics susceptibilities were tested using the recommendations of the Clinical Laboratories Standards Institute. Predictions of emerging resistant bacteria patterns and outbreaks in Sudan were done using logistic regression, forecasting linear equations and in silico simulations models.

Results

A total of 124 antibiotics resistant Salmonella Typhi strains categorized in 12 average groups were isolated, different patterns of resistance statistically calculated by (y = ax − b). Minimum bactericidal concentration’s predication of resistance was given the exponential trend (y = n e^x) and the predictive coefficient R² > 0 < 1 are approximately alike. It was assumed that resistant bacteria occurred with a constant rate of antibiotic doses during the whole experimental period. Thus, the number of sensitive bacteria decreases at the same rate as resistant occur following term to the modified predictive model which solved computationally.

Conclusion

This study assesses the prediction of multi-drug resistance among S. Typhi isolates by applying low cost materials and simple statistical methods suitable for the most frequently used antibiotics as typhoid empirical therapy. Therefore, bacterial surveillance systems should be implemented to present data on the aetiology and current antimicrobial drug resistance patterns of community-acquired agents causing outbreaks.

Electronic supplementary material

The online version of this article (10.1186/s12941-017-0247-4) contains supplementary material, which is available to authorized users.

Biological weathering and the long-term carbon cycle: integrating mycorrhizal evolution and function into the current paradigm

The dramatic decline in atmospheric CO2 evidenced by proxy data during the Devonian (416.0-359.2 Ma) and the gradual decline from the Cretaceous (145.5-65.5 Ma) onwards have been linked to the spread of deeply rooted trees and the rise of angiosperms, respectively. But this paradigm overlooks the coevolution of roots with the major groups of symbiotic fungal partners that have dominated terrestrial ecosystems throughout Earth history. The colonization of land by plants was coincident with the rise of arbuscular mycorrhizal fungi (AMF),while the Cenozoic (c. 65.5-0 Ma) witnessed the rise of ectomycorrhizal fungi (EMF) that associate with both gymnosperm and angiosperm tree roots. Here, we critically review evidence for the influence of AMF and EMF on mineral weathering processes. We show that the key weathering processes underpinning the current paradigm and ascribed to plants are actually driven by the combined activities of roots and mycorrhizal fungi. Fuelled by substantial amounts of recent photosynthate transported from shoots to roots, these fungi form extensive mycelial networks which extend into soil actively foraging for nutrients by altering minerals through the acidification of the immediate root environment. EMF aggressively weather minerals through the additional mechanism of releasing low molecular weight organic chelators. Rates of biotic weathering might therefore be more usefully conceptualized as being fundamentally controlled by the biomass, surface area of contact, and capacity of roots and their mycorrhizal fungal partners to interact physically and chemically with minerals. All of these activities are ultimately controlled by rates of carbon-energy supply from photosynthetic organisms. The weathering functions in leading carbon cycle models require experiments and field studies of evolutionary grades of plants with appropriate mycorrhizal associations. Representation of the coevolution of roots and fungi in geochemical carbon cycle models is required to further our understanding of the role of the biota in Earth's CO2 and climate history.

Application of membrane inlet mass spectrometry for online and in situ analysis of methane in aquatic environments

A method is presented for the online measurement of methane in aquatic environments by application of membrane inlet mass spectrometry (MIMS). For this purpose, the underwater mass spectrometer Inspectr200-200 was applied. A simple and reliable volumetric calibration technique, based on the mixing of two end member concentrations, was used for the analysis of CH(4) by MIMS. To minimize interferences caused by the high water vapor content, permeating through the membrane inlet system into the vacuum section of the mass spectrometer, a cool-trap was designed. With the application of the cool-trap, the detection limit was lowered from 100 to 16 nmol/L CH(4). This allows for measurements of methane concentrations in surface and bottom waters of coastal areas and lakes. Furthermore, in case of membrane rupture, the cool-trap acts as a security system, avoiding total damage of the mass spectrometer by flushing it with water. The Inspectr200-200 was applied for studies of methane and carbon dioxide concentrations in coastal areas of the Baltic Sea and Lake Constance. The low detection limit and fast response time of the MIMS allowed a detailed investigation of methane concentrations in the vicinity of gas seepages.

A review of stable isotope techniques for N2O source partitioning in soils: recent progress, remaining challenges and future considerations

Nitrous oxide is produced in soil during several processes, which may occur simultaneously within different micro-sites of the same soil. Stable isotope techniques have a crucial role to play in the attribution of N(2)O emissions to different microbial processes, through estimation (natural abundance, site preference) or quantification (enrichment) of processes based on the (15)N and (18)O signatures of N(2)O determined by isotope ratio mass spectrometry. These approaches have the potential to become even more powerful when linked with recent developments in secondary isotope mass spectrometry, with microbial ecology, and with modelling approaches, enabling sources of N(2)O to be considered at a wide range of scales and related to the underlying microbiology. Such source partitioning of N(2)O is inherently challenging, but is vital to close the N(2)O budget and to better understand controls on the different processes, with a view to developing appropriate management practices for mitigation of N(2)O. In this respect, it is essential that as many of the contributing processes as possible are considered in any study aimed at source attribution, as mitigation strategies for one process may not be appropriate for another. To aid such an approach, here the current state of the art is critically examined, remaining challenges are highlighted, and recommendations are made for future direction.

The impact of sludge amendment on gas dynamics in an upland soil: monitored by membrane inlet mass spectrometry

Studies of the land disposal of biosolids and municipal sewage have focused largely on the potential pollution of the soil with pathogens, toxic compounds or heavy metals. Little is known about the impact of sludge amendment on carbon source and sink concentrations in soils. In this study gas concentrations in Scottish soil cores (from limed and unlimed plots) were monitored continuously at 3 cm depth before, during and after sludge application using membrane inlet mass spectrometry (MIMS). Following sludge application to soil cores, significant and sustained increases in CH4 (for 8 days) and CO2 (for between 16 and 120 days) concentration were observed. This suggested short-term stimulation of indigenous methanogens, provision of a new methanogenic inoculum, or inhibition of methane oxidizers (for example by heavy metals or NH4 in sludge). Soil microbial fermentative activity was enhanced over periods of a few months as shown by elevated CO2 concentrations.

Flux and turnover of fixed carbon in soil microbial biomass of limed and unlimed plots of an upland grassland ecosystem

The influence of liming on rhizosphere microbial biomass C and incorporation of root exudates was studied in the field by in situ pulse labelling of temperate grassland vegetation with (13)CO(2) for a 3-day period. In plots that had been limed (CaCO(3) amended) annually for 3 years, incorporation into shoots and roots was, respectively, greater and lower than in unlimed plots. Analysis of chloroform-labile C demonstrated lower levels of (13)C incorporation into microbial biomass in limed soils compared to unlimed soils. The turnover of the recently assimilated (13)C compounds was faster in microbial biomass from limed than that from unlimed soils, suggesting that liming increases incorporation by microbial communities of root exudates. An exponential decay model of (13)C in total microbial biomass in limed soils indicated that the half-life of the tracer within this carbon pool was 4.7 days. Results are presented and discussed in relation to the absolute values of (13)C fixed and allocated within the plant-soil system.