- Volume 4, Issue 1, 2022

Sphingolipids, a class of amino-alcohol-based lipids, are well characterized in eukaryotes and in some anaerobic bacteria. However, the only sphingolipids so far identified in cyanobacteria are two ceramides (i.e., an acetylsphingomyelin and a cerebroside), both based on unbranched, long-chain base (LCB) sphingolipids in Scytonema julianum and Moorea producens , respectively. The first step in de novo sphingolipid biosynthesis is the condensation of l-serine with palmitoyl-CoA to produce 3-keto-diyhydrosphingosine (KDS). This reaction is catalyzed by serine palmitoyltransferase (SPT), which belongs to a small family of pyridoxal phosphate-dependent α-oxoamine synthase (AOS) enzymes. Based on sequence similarity to molecularly characterized bacterial SPT peptides, we identified a putative SPT (Npun_R3567) from the model nitrogen-fixing, plant-symbiotic cyanobacterium, Nostoc punctiforme strain PCC 73102 (ATCC 29133). Gene expression analysis revealed that Npun_R3567 is induced during late-stage diazotrophic growth in N. punctiforme . However, Npun_R3567 could not produce the SPT reaction product, 3-keto-diyhydrosphingosine (KDS), when heterologously expressed in Escherichia coli . This agreed with a sphingolipidomic analysis of N. punctiforme cells, which revealed that no LCBs or ceramides were present. To gain a better understanding of Npun_R3567, we inferred the phylogenetic position of Npun_R3567 relative to other bacterial AOS peptides. Rather than clustering with other bacterial SPTs, Npun_R3567 and the other cyanobacterial BioF homologues formed a separate, monophyletic group. Given that N. punctiforme does not appear to possess any other gene encoding an AOS enzyme, it is altogether unlikely that N. punctiforme is capable of synthesizing sphingolipids. In the context of cross-kingdom symbiosis signalling in which sphingolipids are emerging as important regulators, it appears unlikely that sphingolipids from N. punctiforme play a regulatory role during its symbiotic association with plants.

Coral reefs are declining due to anthropogenic disturbances, including climate change. Therefore, improving our understanding of coral ecosystems is vital, and the influence of bacteria on coral health has attracted particular interest. However, a gnotobiotic coral model that could enhance studies of coral–bacteria interactions is absent. To address this gap, we tested the ability of treatment with seven antibiotics for 3 weeks to deplete bacteria in Exaiptasia diaphana, a sea anemone widely used as a coral model. Digital droplet PCR (ddPCR) targeting anemone Ef1-α and bacterial 16S rRNA genes was used to quantify bacterial load, which was found to decrease six-fold. However, metabarcoding of bacterial 16S rRNA genes showed that alpha and beta diversity of the anemone-associated bacterial communities increased significantly. Therefore, gnotobiotic E. diaphana with simplified, uniform bacterial communities were not generated, with biofilm formation in the culture vessels most likely impeding efforts to eliminate bacteria. Despite this outcome, our work will inform future efforts to create a much needed gnotobiotic coral model.

Salmonella enterica subspecies enterica serovar Corvallis (S. Corvallis) has been identified as a human pathogen and as a food contaminant. Diarrhoeal disease is a common diagnosis in tourists visiting Southeast Asia, often with unknown aetiology. However, numerous public health institutes have identified Salmonella as a common causative agent when consuming contaminated food and water. Genomic data from environmental isolates from a Cambodian informal market were uploaded to the National Center for Biotechnology Information (NCBI) platform, allowing the novel sequences to be compared to global whole-genome sequence archives. The comparison revealed that two human clinical isolates from England and four of the environmental isolates were closely related, with an average single nucleotide polymorphism (SNP) difference of 1 (0–3 SNPs). A maximum-likelihood tree based on core SNPs was generated comparing the 4 isolates recovered from a Cambodian informal market with 239 isolates of S. Corvallis received from routine surveillance of human salmonellosis in England and confirmed the close relationship. In addition, the environmental isolates clustered into a broader phylogenetic group within the S. Corvallis population containing 68 additional human isolates, of which 42 were from patients who reported recent international travel, almost exclusively to Southeast Asia. The environmental isolates of S. Corvallis isolated from an informal market in Cambodia are concerning for public health due to their genetic similarity to isolates (e.g. clinical isolates from the UK) with known human virulence and pathogenicity. This study emphasizes the benefits of global and public data sharing of pathogen genomes.

Sewage-based surveillance for COVID-19 has been described in multiple countries and multiple settings. However, nearly all are based on testing sewage treatment plant inflows and outflows using structured sewage networks and treatment systems. Many resource-limited countries worldwide have open canals, lakes and other such waste-contaminated water bodies that act as a means of sewage effluent discharge. These could serve as hyperlocal testing points for detecting COVID-19 incidence using the effluents from nearby communities. However, a sensitive, robust and economical method of SARS-CoV-2 RNA detection from open waste contaminated water bodies in resource-constrained regions is currently lacking. A protocol employed in Bangalore, India, where SARS-CoV-2 RNA levels were evaluated using two open canal systems during the first and second waves in the present study. SARS-CoV-2 RNA was measured using two strategies: a modified TrueNATTM microchip-based rapid method and traditional real-time reverse transcription-PCR (rRT-PCR), which were compared for analytical sensitivity, cost and relative ease of use. SARS-CoV-2 RNA levels were detected at lower levels during the earlier half compared to the later half of the first wave in 2020. The opposite trend was seen in the second wave in 2021. Interestingly, the change in RNA levels corresponded with the community burden of COVID-19 at both sites. The modified TrueNATTM method yielded concordant results to traditional rRT-PCR in sensitivity and specificity and cost. It provides a simple, cost-effective method for detecting and estimating SARS-CoV-2 viral RNA from open-water sewage canals contaminated with human excreta and industrial waste that can be adopted in regions or countries that lack structured sewage systems.

Vegetation complexity is potentially important for urban green space designs aimed at fostering microbial biodiversity to benefit human health. Exposure to urban microbial biodiversity may influence human health outcomes via immune training and regulation. In this context, improving human exposure to microbiota via biodiversity-centric urban green space designs is an underused opportunity. There is currently little knowledge on the association between vegetation complexity (i.e. diversity and structure) and soil microbiota of urban green spaces. Here, we investigated the association between vegetation complexity and soil bacteria in urban green spaces in Bournemouth, UK; Haikou, China; and the City of Playford, Australia by sequencing the 16S rRNA V4 gene region of soil samples and assessing bacterial diversity. We characterized these green spaces as having ‘low’ or ‘high’ vegetation complexity and explored whether these two broad categories contained similar bacterial community compositions and diversity around the world. Within cities, we observed significantly different alpha and beta diversities between vegetation complexities; however, these results varied between cities. Rare genera (<1% relative abundance individually, on average 35% relative abundance when pooled) were most likely to be significantly different in sequence abundance between vegetation complexities and therefore explained much of the differences in microbial communities observed. Overall, general associations exist between soil bacterial communities and vegetation complexity, although these are not consistent between cities. Therefore, more in-depth work is required to be done locally to derive practical actions to assist the conservation and restoration of microbial communities in urban areas.

Human norovirus (HuNoV) is a highly contagious pathogenic virus that is transmitted through contaminated food, water, high-touch surfaces and aerosols. Globally, there are an estimated 685 million infections annually due to norovirus, including 200 million affecting children under the age of 5. HuNoV causes approximately 50, 000 child deaths per year and costs an estimated USD $60 billion annually in healthcare. This study sought to determine the inactivation profile of ultraviolet subtype C (UVC) against norovirus using a UVC light-emitting diode (LED) array, KL265-50V-SM-WD. The array emitted radiation at 269 nm peak wavelength and a measured fluence of 1.25 mW cm−2 at a 7 cm source–surface distance. Since the HuNoV is not cultivable, the study utilized feline calicivirus (FCV) ATCC VR-782, a recommended surrogate as challenge organism. The test followed modified ASTM E2197. Assessment of virus inactivation was performed using a plaque assay method. With irradiance at a UVC dose of 22.5 mJ cm−2, the study obtained 99.9 % virus reduction (3 log reduction). The results demonstrate that the UVC LED array can provide effective inactivation of HuNoV.