Small RNAs (sRNAs) from conserved noncoding genes are crucial regulators in bacterial signaling pathways but have remained elusive in the Cpx response to inner membrane stress. Here we report that an ...alternative biogenesis pathway releasing the conserved mRNA 3′ UTR of stress chaperone CpxP as an ∼60-nt sRNA provides the noncoding arm of the Cpx response. This so-called CpxQ sRNA, generated by general mRNA decay through RNase E, acts as an Hfq-dependent repressor of multiple mRNAs encoding extracytoplasmic proteins. Both CpxQ and the Cpx pathway are required for cell survival under conditions of dissipation of membrane potential. Our discovery of CpxQ illustrates how the conversion of a transcribed 3′ UTR into an sRNA doubles the output of a single mRNA to produce two factors with spatially segregated functions during inner membrane stress: a chaperone that targets problematic proteins in the periplasm and a regulatory RNA that dampens their synthesis in the cytosol.
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•RNase E cleaves the 3′ end of cpxP mRNA to release a small RNA, CpxQ•CpxQ together with the Hfq protein represses mRNAs of envelope proteins•CpxQ and the Cpx pathway protect bacteria against inner membrane damage•Cytosolic activity of CpxQ sRNA complements periplasmic function of CpxP protein
Chao and Vogel discover that a small RNA cleaved off the 3′ end of an mRNA provides the elusive regulatory noncoding arm of the bacterial Cpx response to inner membrane stress.
The transcriptome is a powerful proxy for the physiological state of a cell, healthy or diseased. As a result, transcriptome analysis has become a key tool in understanding the molecular changes that ...accompany bacterial infections of eukaryotic cells. Until recently, such transcriptomic studies have been technically limited to analyzing mRNA expression changes in either the bacterial pathogen or the infected eukaryotic host cell. However, the increasing sensitivity of high-throughput RNA sequencing now enables "dual RNA-seq" studies, simultaneously capturing all classes of coding and noncoding transcripts in both the pathogen and the host. In the five years since the concept of dual RNA-seq was introduced, the technique has been applied to a range of infection models. This has not only led to a better understanding of the physiological changes in pathogen and host during the course of an infection but has also revealed hidden molecular phenotypes of virulence-associated small noncoding RNAs that were not visible in standard infection assays. Here, we use the knowledge gained from these recent studies to suggest experimental and computational guidelines for the design of future dual RNA-seq studies. We conclude this review by discussing prospective applications of the technique.
The relaxation dynamics toward a hydrostatic equilibrium after a change in phase saturation in porous media is governed by fluid reconfiguration at the pore scale. Little is known whether a ...hydrostatic equilibrium in which all interfaces come to rest is ever reached and which microscopic processes govern the time scales of relaxation. Here we apply fast synchrotron‐based X‐ray tomography (X‐ray CT) to measure the slow relaxation dynamics of fluid interfaces in a glass bead pack after fast drainage of the sample. The relaxation of interfaces triggers internal redistribution of fluids, reduces the surface energy stored in the fluid interfaces, and relaxes the contact angle toward the equilibrium value while the fluid topology remains unchanged. The equilibration of capillary pressures occurs in two stages: (i) a quick relaxation within seconds in which most of the pressure drop that built up during drainage is dissipated, a process that is to fast to be captured with fast X‐ray CT, and (ii) a slow relaxation with characteristic time scales of 1–4 h which manifests itself as a spontaneous imbibition process that is well described by the Washburn equation for capillary rise in porous media. The slow relaxation implies that a hydrostatic equilibrium is hardly ever attained in practice when conducting two‐phase experiments in which a flux boundary condition is changed from flow to no‐flow. Implications for experiments with pressure boundary conditions are discussed.
Plain Language Summary
What happens to fluids in a porous medium after pumping is stopped? Fast X‐ray tomography shows that even in a sample smaller than a sugar cube fluid interfaces continue to move for hours until an optimal fluid configuration is reached. The pace is limited by slow relaxation of dynamic contact angles. Therefore hydrostatic equilibrium, which is the state at which all fluid interfaces come to rest, is hardly ever attained in practice when conducting two‐phase flow experiments where the flow is stopped in much larger soil or rock samples.
Key Points
Relaxation dynamics through internal redistribution of fluids after fast drainage occurs in two stages
A quick dissipation within seconds is followed by slow relaxation within several hours due to relaxation of dynamic contact angles
Fluid configurations during relaxation are very different from those during quasi‐static drainage and imbibition
Abstract
Over the past two decades, small noncoding RNAs (sRNAs) that regulate mRNAs by short base pairing have gone from a curiosity to a major class of post-transcriptional regulators in bacteria. ...They are integral to many stress responses and regulatory circuits, affecting almost all aspects of bacterial life. Following pioneering sRNA searches in the early 2000s, the field quickly focused on conserved sRNA genes in the intergenic regions of bacterial chromosomes. Yet, it soon emerged that there might be another rich source of bacterial sRNAs—processed 3′ end fragments of mRNAs. Several such 3′ end-derived sRNAs have now been characterized, often revealing unexpected, conserved functions in diverse cellular processes. Here, we review our current knowledge of these 3′ end-derived sRNAs—their biogenesis through ribonucleases, their molecular mechanisms, their interactions with RNA-binding proteins such as Hfq or ProQ and their functional scope, which ranges from acting as specialized regulators of single metabolic genes to constituting entire noncoding arms in global stress responses. Recent global RNA interactome studies suggest that the importance of functional 3′ end-derived sRNAs has been vastly underestimated and that this type of cross-regulation between genes at the mRNA level is more pervasive in bacteria than currently appreciated.
There are a growing number of examples of bacterial mRNAs that produce small RNAs cleaved from their own 3′ ends to post-transcriptionally control other genes.
RNA is involved in the regulation of multiple cellular processes, often by forming sequence-specific base pairs with cellular RNA or DNA targets that must be identified among the large number of ...nucleic acids in a cell. Several RNA-based regulatory systems in eukaryotes, bacteria and archaea, including microRNAs (miRNAs), small interfering RNAs (siRNAs), CRISPR RNAs (crRNAs) and small RNAs (sRNAs) that are dependent on the RNA chaperone protein Hfq, achieve specificity using similar strategies. Central to their function is the presentation of short 'seed sequences' within a ribonucleoprotein complex to facilitate the search for and recognition of targets.
The capacity of soils to store organic carbon represents a key function of soils that is not only decisive for climate regulation but also affects other soil functions. Recent efforts to assess the ...impact of land management on soil functionality proposed that an indicator- or proxy-based approach is a promising alternative to quantify soil functions compared to time- and cost-intensive measurements, particularly when larger regions are targeted. The objective of this review is to identify measurable biotic or abiotic properties that control soil organic carbon (SOC) storage at different spatial scales and could serve as indicators for an efficient quantification of SOC. These indicators should enable both an estimation of actual SOC storage as well as a prediction of the SOC storage potential, which is an important aspect in land use and management planning. There are many environmental conditions that affect SOC storage at different spatial scales. We provide a thorough overview of factors from micro-scales (particles to pedons) to the global scale and discuss their suitability as indicators for SOC storage: clay mineralogy, specific surface area, metal oxides, Ca and Mg cations, microorganisms, soil fauna, aggregation, texture, soil type, natural vegetation, land use and management, topography, parent material and climate. As a result, we propose a set of indicators that allow for time- and cost-efficient estimates of actual and potential SOC storage from the local to the regional and subcontinental scale. As a key element, the fine mineral fraction was identified to determine SOC stabilization in most soils. The quantification of SOC can be further refined by including climatic proxies, particularly elevation, as well as information on land use, soil management and vegetation characteristics. To enhance its indicative power towards land management effects, further “functional soil characteristics”, particularly soil structural properties and changes in the soil microbial biomass pool should be included in this indicator system. The proposed system offers the potential to efficiently estimate the SOC storage capacity by means of simplified measures, such as soil fractionation procedures or infrared spectroscopic approaches.
•Indicators for current and potential SOC storage at various scales were identified•An indicator system for SOC storage from local to regional scales is proposed•The fine mineral fraction was identified as a key indicator•Soil structural properties and microbial biomass are further promising indicators•Simplified soil fractionation or infrared spectroscopic approaches are needed
Core Ideas
The soil profile is the critical scale for representation of soil hydrology also at larger scales.
Natural soils do not follow well‐defined hydraulic properties.
Concepts are needed to ...model hydraulic nonequilibrium and hysteresis.
Spatial patterns of functional soil types need to be identified.
These can account for vertical stratification of hydraulic properties and structural attributes.
Soil hydrology is a key control for the functioning of the terrestrial environment. Many environmental issues that we need to tackle today are directly linked to soil water dynamics. This includes agricultural production and food security, nutrient cycling and carbon storage, prevention of soil degradation and erosion, and last but not least, clean water resources and flood protection. However, these problems need to be addressed at the scales of fields, regions, and landscapes, while soil water dynamics and soil hydraulic properties are well understood and typically measured at much smaller scales—the comfort zone of soil physics. An obvious problem is how to link these vastly different scales and how to profit from small‐scale understanding to improve our capability to predict what is going on at the large scale. In this update, this problem is discussed based on insights gained during the last decades. As a synthesis, a two‐step scaling approach is proposed for modeling soil water dynamics from local to landscape scales where the scale of the soil profile is the stepping stone.
Salmonella species are enterobacterial pathogens that have been exceptionally well investigated with respect to virulence mechanisms, microbial pathogenesis, genome evolution and many fundamental ...pathways of gene expression and metabolism. While these studies have traditionally focused on protein functions, Salmonella has also become a model organism for RNA-mediated regulation. The present review is dedicated to the non-coding RNA world of Salmonella: it covers small RNAs (sRNAs) that act as post-transcriptional regulators of gene expression, novel Salmonella cis-regulatory RNA elements that sense metabolite and metal ion concentrations (or temperature), and globally acting RNA-binding proteins such as CsrA or Hfq (inactivation of which cause drastic phenotypes and virulence defects). Owing to mosaic genome structure, some of the Salmonella sRNAs are widely conserved in bacteria whereas others are very specific to Salmonella species. Intriguingly, sRNAs of either type (CsrB/C, InvR, SgrS) facilitate cross-talk between the Salmonella core genome and its laterally acquired virulence regions. Work in Salmonella also identified physiological functions (and mechanisms thereof) of RNA that had remained unknown in Escherichia coli, and pioneered the use of high-throughput sequencing technology to identify the sRNA and mRNA targets of bacterial RNA-binding proteins.
During soil formation, the interaction of different biota (plants, soil fauna, microbes) with weathered mineral material shapes unique structures depending on the parental material and the site ...specific climatic conditions. While many of these interactions are known, the relative importance of the different biota is difficult to unravel and therefore difficult to quantify. Biological soil structure formation is often superimposed by soil management and swell-shrink dynamics, making it even more difficult to derive mechanistic understanding.
We here explore soil structure formation within a “space-for-time” chronosequence in the Rhenish lignite mining area. Loess material from a depth of 4–10 m has been used for reclamation in a standardized procedure for 24 years.
Changes in soil pore system are characterized by properties such as connectivity (Euler number) and pore size distribution using undisturbed soil columns with a diameter of 10 cm. They were taken from two different depths (0–20 cm and 40–60 cm) at different sites ranging in age from 0 to 24 years. X-ray CT is used for scanning the original columns as well as undisturbed subsamples of 3 and 0.7 cm diameter. This hierarchical sampling scheme was developed to overcome the trade-off between sample size and resolution.
For the first time also information on the development of biopores could be measured by separating them from other structural pores based on their unique shape. The data were complemented by destructive sampling and determination of root length with WinRHIZO to give an estimate of how many biopores are filled with roots. Furthermore HYPROP measurements of water retention curves were conducted and showed a general agreement with the image-derived pore size distribution merged across three scales.
An increase in biopore density throughout year zero to year 12, in particular in 40–60 cm soil depth, was observed. The biopore length densities of approximately 17 cm/cm3 obtained in year 12 was similar to the one measured in year 24, suggesting that equilibrium was reached. Only about 10% of these biopores were filled with roots. In the topsoil (0–20 cm) the equilibrium value in biopore density is already reached after six years due to a higher root length density. Ploughing lead to higher mean pore size and to lower connectivity compared to the well-connected, very stable pore network in 40–60 cm depth.
This study shows how fast plant roots create a stable and connected biopore system and how this is disrupted by soil tillage, which produces completely contrasting pore characteristics.
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•X-ray μCT disentangles effect of tillage and plant roots on soil structure over time.•A new segmentation method allowed for quantification of biopore-network•A maximum biopore density (18 cm cm−3) was already reached after 6 years 18 cm cm−3.•Tillage led to total different macropore characteristics.
Highlights • RNA-seq has become the method of choice for bacterial transcriptomics. • Differential RNA-seq (dRNA-seq) distinguishes primary and processed transcripts. • dRNA-seq provides global TSS ...maps and other transcriptome information. • dRNA-seq is generic and has been applied to many different species.
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