Freshwater monitoring by nanopore sequencing.

While traditional microbiological freshwater tests focus on the detection of specific bacterial indicator species, including pathogens, direct tracing of all aquatic DNA through metagenomics poses a profound alternative. Yet, in situ metagenomic water surveys face substantial challenges in cost and logistics. Here, we present a simple, fast, cost-effective and remotely accessible freshwater diagnostics workflow centred around the portable nanopore sequencing technology. Using defined compositions and spatiotemporal microbiota from surface water of an example river in Cambridge (UK), we provide optimised experimental and bioinformatics guidelines, including a benchmark with twelve taxonomic classification tools for nanopore sequences. We find that nanopore metagenomics can depict the hydrological core microbiome and fine temporal gradients in line with complementary physicochemical measurements. In a public health context, these data feature relevant sewage signals and pathogen maps at species level resolution. We anticipate that this framework will gather momentum for new environmental monitoring initiatives using portable devices

Integrating Suspended Sediment Flux in Large Alluvial River Channels: Application of a Synoptic Rouse‐Based Model to the Irrawaddy and Salween Rivers

A large portion of freshwater and sediment is exported to the ocean by a small number of major rivers. Many of these megarivers are subject to substantial anthropogenic pressures, which are having a major impact on water and sediment delivery to deltaic ecosystems. Due to hydrodynamic sorting, sediment grain size and composition vary strongly with depth and across the channel in large rivers, complicating flux quantification. To account for this, we modified a semi‐empirical Rouse model, synoptically predicting sediment concentration, grain‐size distribution, and organic carbon (%OC) concentration with depth and across the river channel. Using suspended sediment depth samples and flow velocity data, we applied this model to calculate sediment fluxes of the Irrawaddy (Ayeyarwady) and the Salween (Thanlwin), the last two free‐flowing megarivers in Southeast Asia. Deriving sediment‐discharge rating curves, we calculated an annual sediment flux of urn:x-wiley:jgrf:media:jgrf21236:jgrf21236-math-0001 Mt/year for the Irrawaddy and urn:x-wiley:jgrf:media:jgrf21236:jgrf21236-math-0002 Mt/year for the Salween, together exporting 46% as much sediment as the Ganges‐Brahmaputra system. The mean flux‐weighted sediment exported by the Irrawaddy is significantly coarser (D84 = 193 ± 13 μm) and OC‐poorer (0.29 ± 0.08 wt%) compared to the Salween (112 ± 27 μm and 0.59 ± 0.16 wt%, respectively). Both rivers export similar amounts of particulate organic carbon, with a total of urn:x-wiley:jgrf:media:jgrf21236:jgrf21236-math-0003 Mt C/year, 53% as much as the Ganges‐Brahmaputra. These results underline the global significance of the Irrawaddy and Salween rivers and warrant continued monitoring of their sediment flux, given the increasing anthropogenic pressures on these river basins

Global silicate weathering flux overestimated because of sediment–water cation exchange

Rivers carry the dissolved and solid products of silicate mineral weathering, a process that removes CO2 from the atmosphere and provides a key negative climate feedback over geological timescales. Here we show that in some river systems, a reactive exchange pool on river suspended particulate matter, bonded weakly to mineral surfaces, increases the mobile cation flux by 50%. The chemistry of both river waters and the exchange pool demonstrate exchange equilibrium, confirmed by Sr isotopes. Global silicate weathering fluxes are calculated based on riverine dissolved sodium (Na+) from silicate minerals. The large exchange pool supplies Na+ of non- silicate origin to the dissolved load, especially in catchments with widespread marine sediments, or where rocks have equilibrated with saline basement fluids. We quantify this by comparing the riverine sediment exchange pool and river water chemistry. In some basins, cation exchange could account for the majority of sodium in the river water, significantly reducing estimates of silicate weathering. At a global scale, we demonstrate that silicate weathering fluxes are over-estimated by 12-28%. This over-estimation is greatest in regions of high erosion and high sediment loads where the negative climate feedback has a maximum sensitivity to chemical weathering reactions. In the context of other recent findings that reduce the net CO2 consumption through chemical weathering, the magnitude of the continental silicate weathering fluxes and its implications for solid Earth CO2 degassing fluxes needs to be further investigated

Vascular tube formation on matrix metalloproteinase-1-damaged collagen

Connective tissue damage and angiogenesis are both important features of tumour growth and invasion. Here, we show that endothelial cells maintained on a three-dimensional lattice of intact polymerised collagen formed a monolayer of cells with a cobblestone morphology. When the collagen was exposed to organ culture fluid from human basal cell tumours of the skin (containing a high level of active matrix metalloproteinase-1 (MMP-1)), degradation of the collagen matrix occurred. The major degradation products were the $3over 4$- and $1over 4$-sized fragments known to result from the action of MMP-1 on type I collagen. When endothelial cells were maintained on the partially degraded collagen, the cells organised into a network of vascular tubes. Pretreatment of the organ culture fluid with either tissue inhibitor of metalloproteinase-1 (TIMP-1) or neutralising antibody to MMP-1 prevented degradation of the collagen lattice and concomitantly inhibited endothelial cell organisation into the vascular network. Purified (activated) MMP-1 duplicated the effects of skin organ culture fluid, but other enzymes including MMP-9 (gelatinase B), elastase or trypsin failed to produce measurable fragments from intact collagen and also failed to promote vascular tube formation. Together, these studies suggest that damage to the collagenous matrix is itself an important inducer of new vessel formation

Freshwater monitoring by nanopore sequencing

Many water-dwelling bacteria can cause severe diseases such as cholera, typhoid or leptospirosis. One way to prevent outbreaks is to test water sources to find out which species of microbes they contain, and at which levels. Traditionally, this involves taking a water sample, followed by growing a few species of ‘indicator bacteria’ that help to estimate whether the water is safe. An alternative technique, called metagenomics, has been available since the mid-2000s. It consists in reviewing (or ‘sequencing’) the genetic information of most of the bacteria present in the water, which allows scientists to spot harmful species. Both methods, however, require well-equipped laboratories with highly trained staff, making them challenging to use in remote areas. The MinION is a pocket-sized device that – when paired with a laptop or mobile phone – can sequence genetic information ‘on the go’. It has already been harnessed during Ebola, Zika or SARS-CoV-2 epidemics to track the genetic information of viruses in patients and environmental samples. However, it is still difficult to use the MinION and other sequencers to monitor bacteria in water sources, partly because the genetic information of the microbes is highly fragmented during DNA extraction. To address this challenge, Urban, Holzer et al. set out to optimise hardware and software protocols so the MinION could be used to detect bacterial species present in rivers. The tests focussed on the River Cam in Cambridge, UK, a waterway which faces regular public health problems: local rowers and swimmers often contract waterborne infections, sometimes leading to river closures. For six months, Urban, Holzer et al. used the MinION to map out the bacteria present across nine river sites, assessing the diversity of species and the presence of disease-causing microbes in the water. In particular, the results showed that optimising the protocols made it possible to tell the difference between closely related species – an important feature since harmful and inoffensive bacteria can sometimes be genetically close. The data also revealed that the levels of harmful bacteria were highest downstream of urban river sections, near a water treatment plant and river barge moorings. Together, these findings demonstrate that optimising MinION protocols can turn this device into a useful tool to easily monitor water quality. Around the world, climate change, rising urbanisation and the intensification of agriculture all threaten water quality. In fact, access to clean water is one of the United Nations sustainable development goals for 2030. Using the guidelines developed by Urban, Holzer et al., communities could harness the MinION to monitor water quality in remote areas, offering a cost-effective, portable DNA analysis tool to protect populations against deadly diseases

Global silicate weathering flux overestimated because of sediment–water cation exchange

Rivers carry the dissolved and solid products of silicate mineral weathering, a process that removes CO2 from the atmosphere and provides a key negative climate feedback over geological timescales. Here we show that, in some river systems, a reactive exchange pool on river suspended particulate matter, bonded weakly to mineral surfaces, increases the mobile cation flux by 50%. The chemistry of both river waters and the exchange pool demonstrates exchange equilibrium, confirmed by Sr isotopes. Global silicate weathering fluxes are calculated based on riverine dissolved sodium (Na+) from silicate minerals. The large exchange pool supplies Na+ of nonsilicate origin to the dissolved load, especially in catchments with widespread marine sediments, or where rocks have equilibrated with saline basement fluids. We quantify this by comparing the riverine sediment exchange pool and river water chemistry. In some basins, cation exchange could account for the majority of sodium in the river water, significantly reducing estimates of silicate weathering. At a global scale, we demonstrate that silicate weathering fluxes are overestimated by 12 to 28%. This overestimation is greatest in regions of high erosion and high sediment loads where the negative climate feedback has a maximum sensitivity to chemical weathering reactions. In the context of other recent findings that reduce the net CO2 consumption through chemical weathering, the magnitude of the continental silicate weathering fluxes and its implications for solid Earth CO2 degassing fluxes need to be further investigated

Application of binomial coefficients in representing central difference solution to a class of PDE arising in chemistry

10.1007/s10910-005-9011-7Journal of Mathematical Chemistry391177-18