Carbon dots for staining bacterial dead cells and distinguishing dead/alive bacteria.

The small molecular dyes such as propidium iodide (PI) always suffer from photo-bleaching and potential toxicity. To tackle the problems, a type of nontoxic carbon dots (CDs) was obtained for dead/alive bacterial distinguishing. This kind of carbon dots has an average size of 1.91 nm and owns carboxyl groups, emerging as excellent candidates for imaging bacterial cells. The negative charges of carboxyl groups lead their avoidance of alive cells while their small size facilitates penetration of dead cells. This kind of nontoxic CDs has effectively differentiated between and alive ones, presenting a highly promising green dye comparing with traditional small molecular dyes.

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.

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.

Microbial Monitoring in the International Space Station and Its Application on Earth.

The space habitat is a confined environment with a simple ecosystem that consists mainly of microorganisms and humans. Changes in the pathogenicity and virulence of bacteria, as well as in astronauts' immune systems, during spaceflight may pose potential hazards to crew health. To ensure microbiological safety in the space habitat, a comprehensive analysis of environmental microbiota is needed to understand the overall microbial world in this habitat. The resulting data contribute to evidence-based microbial monitoring, and continuous microbial monitoring will provide information regarding changes in bioburden and microbial ecosystem; this information is indispensable for microbiological management. Importantly, the majority of microbes in the environment are difficult to culture under conventional culture conditions. To improve understanding of the microbial community in the space habitat, culture-independent approaches are required. Furthermore, there is a need to assess the bioburden and physiological activity of microbes during future long-term space habitation, so that the "alert" and/or "action" level can be assessed based on real-time changes in the microbial ecosystem. Here, we review the microbial monitoring in the International Space Station-Kibo, and discuss how these results will be adapted to the microbial control in space habitation and pharmaceutical and food processing industries.

High-frequency, dielectric spectroscopy for the detection of electrophysiological/biophysical differences in different bacteria types and concentrations.

This paper describes a novel technique to quantify and identify bacterial cultures of Bacillus Subtilis (2.10-1.30 × 109 CFU mL-1) and Escherichia Coli (1.60-1.00 × 109 CFU mL-1), in corn oil using dielectric spectroscopy at elevated frequencies of 0.0100-20.0 GHz. This technique is using the electrophysiological/biophysical differences (e.g. gram positive and gram negative) between various bacteria types, as a basis to distinguish between bacteria concentrations and bacteria types. A close-ended, coaxial probe of 20.0 mm long sample-holder was developed and used to calculate the dielectric constant from the measured S parameters of the bacterial cultures, using the Nicolson-Ross-Weir method. This technique shows a linear relationship (r2 ≥ 0.999) between the dielectric constant and the cell concentration, at 16.0 GHz. The sensitivity of the technique is 0.177 × 109 (CFU mL-1)-1 for B. Subtilis (with a size of 10.0 × 1.00 µm), 0.322 × 109 (CFU mL-1)-1 for E. Coli (with a size of 2.00 × 0.500 µm) and 0.913 × 109 (CFU mL-1) -1 for their 1:1 mixture, while the response time is 60.0s. The dependency of dielectric constant on the bacterial cell concentration at a given frequency can be potentially exploited for measuring bacterial concentrations and biophysical differences.

A convenient purification method for silver nanoclusters and its applications in fluorescent pH sensors for bacterial monitoring.

Herein, we report a convenient approach to purify water-soluble dihydrolipoic acid (DHLA)-capped Ag nanoclusters (Ag NCs) by pH-induced precipitation under acidic conditions. The fluorescence of Ag NCs could be completely recovered by re-dispersing the precipitate into a basic solution using DHLA and NaBH4 as stabilizing ligands and etching reagent. DHLA-Ag NCs-doped agarose hydrogels have been prepared to monitor pH with a wide range from 8.0 to 4.0. When pH decreased, the fluorescence of the hydrogels under a UV lamp decreased and completely disappeared after pH 5. The DHLA-Ag NCs-doped agarose hydrogels biosensor showed low cytotoxicity and long stability. Accordingly, a fluorescent pH sensor for bacterial monitoring has been employed based on the "OFF-ON" signal switch of the Ag NCs-agarose hydrogel.