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Background Water is the most abundant resource on earth, however water scarcity affects more than 40% of people worldwide. Access to safe drinking water is a basic human right and is a United Nations Sustainable Development Goal (SDG) 6. Globally, waterborne diseases such as cholera are responsible for over two million deaths annually. Cholera is a major cause of ill-health in Africa and Uganda. This study aimed to determine the physicochemical characteristics of the surface and spring water in cholera endemic communities of Uganda in order to promote access to safe drinking water. Methods A longitudinal study was carried out between February 2015 and January 2016 in cholera prone communities of Uganda. Surface and spring water used for domestic purposes including drinking from 27 sites (lakes, rivers, irrigation canal, springs and ponds) were tested monthly to determine the vital physicochemical parameters, namely pH, temperature, dissolved oxygen, conductivity and turbidity. Results Overall, 318 water samples were tested. Twenty-six percent (36/135) of the tested samples had mean test results that were outside the World Health Organization (WHO) recommended drinking water range. All sites (100%, 27/27) had mean water turbidity values greater than the WHO drinking water recommended standards and the temperature of above 17 °C. In addition, 27% (3/11) of the lake sites and 2/5 of the ponds had pH and dissolved oxygen respectively outside the WHO recommended range of 6.5–8.5 for pH and less than 5 mg/L for dissolved oxygen. These physicochemical conditions were ideal for survival of Vibrio. cholerae . Conclusions This study showed that surface water and springs in the study area were unsafe for drinking and had favourable physicochemical parameters for propagation of waterborne diseases including cholera. Therefore, for Uganda to attain the SDG 6 targets and to eliminate cholera by 2030, more efforts are needed to promote access to safe drinking water. Also, since this study only established the vital water physicochemical parameters, further studies are recommended to determine the other water physicochemical parameters such as the nitrates and copper. Studies are also needed to establish the causal-effect relationship between V. cholerae and the physicochemical parameters.

Acute hepatopancreatic necrosis disease (AHPND) (formerly, early mortality syndrome) is a high-mortality-rate shrimp disease prevalent in shrimp farming areas. Although AHPND is known to be caused by pathogenic Vibrio parahaemolyticus hosting the plasmid-related PirAB vp toxin gene, the effects of disturbances in microbiome have not yet been studied. We took 62 samples from a grow-out pond during an AHPND developing period from Days 23 to 37 after stocking white postlarvae shrimp and sequenced the 16S rRNA genes with Illumina sequencing technology. The microbiomes of pond seawater and shrimp stomachs underwent varied dynamic succession during the period. Despite copies of PirAB vp , principal co-ordinates analysis revealed two distinctive stages of change in stomach microbiomes associated with AHPND. AHPND markedly changed the bacterial diversity in the stomachs; it decreased the Shannon index by 53.6% within approximately 7 days, shifted the microbiome with Vibrio and Candidatus Bacilloplasma as predominant populations, and altered the species-to-species connectivity and complexity of the interaction network. The AHPND-causing Vibrio species were predicted to develop a co-occurrence pattern with several resident and transit members within Candidatus Bacilloplasma and Cyanobacteria . This study’s insights into microbiome dynamics during AHPND infection can be valuable for minimising this disease in shrimp farming ponds.

Surface mining of enormous oil sands deposits in northeastern Alberta, Canada since 1967 has contributed greatly to Canada's economy but has also received negative international attention due largely to environmental concerns and challenges. Not only have microbes profoundly affected the composition and behavior of this petroleum resource over geological time, they currently influence the management of semi-solid tailings in oil sands tailings ponds (OSTPs) and tailings reclamation. Historically, microbial impacts on OSTPs were generally discounted, but next-generation sequencing and biogeochemical studies have revealed unexpectedly diverse indigenous communities and expanded our fundamental understanding of anaerobic microbial functions. OSTPs that experienced different processing and management histories have developed distinct microbial communities that influence the behavior and reclamation of the tailings stored therein. In particular, the interactions of Deltaproteobacteria and Firmicutes with methanogenic archaea impact greenhouse gas emissions, sulfur cycling, pore water toxicity, sediment biogeochemistry and densification, water usage and the trajectory of long-term mine waste reclamation. This review summarizes historical data; synthesizes current understanding of microbial diversity and activities in situ and in vitro; predicts microbial effects on tailings remediation and reclamation; and highlights knowledge gaps for future research.

Although all plant and animal species harbor microbial symbionts, we know surprisingly little about the specificity of microbial communities to their hosts. Few studies have compared the microbiomes of different species of animals, and fewer still have examined animals in the wild. We sampled four pond habitats in Colorado, USA, where multiple amphibian species were present. In total, 32 amphibian individuals were sampled from three different species including northern leopard frogs ( Lithobates pipiens ), western chorus frogs ( Pseudacris triseriata ) and tiger salamanders ( Ambystoma tigrinum ). We compared the diversity and composition of the bacterial communities on the skin of the collected individuals via barcoded pyrosequencing of the 16S rRNA gene. Dominant bacterial phyla included Acidobacteria , Actinobacteria , Bacteriodetes , Cyanobacteria , Firmicutes and Proteobacteria . In total, we found members of 18 bacterial phyla, comparable to the taxonomic diversity typically found on human skin. Levels of bacterial diversity varied strongly across species: L. pipiens had the highest diversity; A. tigrinum the lowest. Host species was a highly significant predictor of bacterial community similarity, and co-habitation within the same pond was not significant, highlighting that the skin-associated bacterial communities do not simply reflect those bacterial communities found in their surrounding environments. Innate species differences thus appear to regulate the structure of skin bacterial communities on amphibians. In light of recent discoveries that some bacteria on amphibian skin have antifungal activity, our finding suggests that host-specific bacteria may have a role in the species-specific resistance to fungal pathogens.

Small lakes and ponds occupy an enormous surface area of inland freshwater and represent an important terrestrial–water interface. Disturbances caused by extreme weather events can have substantial effects on these ecosystems. Here, we analysed the dynamics of nutrients and the entire plankton community in two flood events and afterwards, when quasi-stable conditions were established, to investigate the effect of such disturbances on a small forest pond. We show that floodings result in repeated washout of resident organisms and hundredfold increases in nutrient load. Despite this, the microbial community recovers to a predisturbance state within two weeks of flooding through four well-defined succession phases. Reassembly of phytoplankton and especially zooplankton takes up to two times longer and features repetitive and adaptive patterns. Release of dissolved nutrients from the pond is associated with inflow rates and community recovery, and returns to predisturbance levels before microbial compositions recover. Our findings shed light on the mechanisms underlying functional resilience of small waterbodies and are relevant to global change-induced increases in weather extremes. Resilience of freshwater microbial communities to flooding is revealed by high-resolution in situ sampling experiments in a forest pond during two extreme rain events.

The hydrocarbon-enriched environments, such as oil reservoirs and oil sands tailings ponds, contain a broad diversity of uncultured microorganisms. Despite being one of the few prokaryotic lineages that is consistently detected in both production water from oil reservoirs and stable hydrocarbon-degrading enrichment cultures originated from oil reservoirs, the physiological and ecological roles of candidate phylum “Atribacteria” (OP9/JS1) are not known in deep subsurface environments. Here, we report the expanded metabolic capabilities of Atribacteria as inferred from genomic reconstructions. Seventeen newly assembled medium-to-high-quality metagenomic assembly genomes (MAGs) were obtained either from co-assembly of two metagenomes from an Alaska North Slope oil reservoir or from previous studies of metagenomes coming from different environments. These MAGs comprise three currently known genus-level lineages and four novel genus-level groups of OP9 and JS1, which expands the genomic coverage of the major lineages within the candidate phylum Atribacteria. Genes involved in anaerobic hydrocarbon degradation were found in seven MAGs associated with hydrocarbon-enriched environments, and suggest that some Atribacteria could ferment short-chain n -alkanes into fatty acid while conserving energy. This study expands predicted metabolic capabilities of Atribacteria (JS1) and suggests that they are mediating a key role in subsurface carbon cycling.

Microplastic pollution in aquatic environments is a growing global concern. Microplastics, defined as plastic fragments smaller than 5 mm, accumulate in freshwater reservoirs, especially in urban areas, impacting resident biota. This study examined the effects of microplastics (MP) on the performance and microbiome of Daphnia, a keystone organism in freshwater ecosystems, through both in situ sampling of freshwater ponds and a controlled 23-day in vitro exposure experiment. Using bacterial 16S ribosomal RNA gene amplicon sequencing and whole-genome shotgun sequencing, we analyzed the microbiome's composition and functional capacity in relation to microplastic pollution levels. Urban ponds contained higher microplastic concentrations in water and sediment than natural ponds, with distinct differences in plastic composition. Bacterioplankton communities, defined as bacterial assemblages in the water column, were more diverse and richer than Daphnia-associated microbiomes. Overall, the in situ study showed that the composition of the Daphnia-associated community was influenced by many factors including microplastic levels but also temperature and redox potential. Functional analysis showed increased relative abundances of polyethylene terephthalate degradation enzymes and antibiotic resistance genes in microbiomes from high-microplastic ponds. In the in vitro experiment, the bacterioplankton inoculum source significantly influenced Daphnia survival and microbiome composition. Network analysis identified specific taxa associated with MP within the Daphnia microbiome. Our findings highlight that urbanization leads to higher microplastic and antibiotic resistance gene burdens, influencing host-associated microbiomes through taxonomic shifts, functional enrichment, and survival outcomes, with potential implications for the resilience of aquatic ecosystems.

Bacterial diseases cause production failures in shrimp aquacultures. To understand environmental conditions and bacterial community dynamics contributing to white faeces disease (WFD) events, we analysed water quality and compared bacterial communities in water as well as in intestines and faeces of healthy and diseased shrimps, respectively, via 16S rRNA gene sequencing and qPCR of transmembrane regulatory protein ( toxR ), thermolabile haemolysin ( tlh ), and thermostable direct haemolysin genes of pathogenic Vibrio parahaemolyticus as a proxy for virulence. WFD occurred when pH decreased to 7.71–7.84, and Alteromonas , Pseudoalteromonas and Vibrio dominated the aquatic bacterial communities. The disease severity further correlated with increased proportions of Alteromonas , Photobacterium, Pseudoalteromonas and Vibrio in shrimp faeces. These opportunistic pathogenic bacteria constituted up to 60% and 80% of the sequences in samples from the early and advances stages of the disease outbreak, respectively, and exhibited a high degree of co-occurrence. Furthermore, toxR and tlh were detected in water at the disease event only. Notably, bacterial community resilience in water occurred when pH was adjusted to 8. Then WFD ceased without a mortality event. In conclusion, pH was a reliable indicator of the WFD outbreak risk. Dissolved oxygen and compositions of water and intestinal bacteria may also serve as indicators for better prevention of WFD events.

Multi-pond salterns constitute an excellent model for the study of the microbial diversity and ecology of hypersaline environments, showing a wide range of salt concentrations, from seawater to salt saturation. Accumulated studies on the Santa Pola (Alicante, Spain) multi-pond solar saltern during the last 35 years include culture-dependent and culture-independent molecular methods and metagenomics more recently. These approaches have permitted to determine in depth the microbial diversity of the ponds with intermediate salinities (from 10 % salts) up to salt saturation, with haloarchaea and bacteria as the two main dominant groups. In this review, we describe the main results obtained using the different methodologies, the most relevant contributions for understanding the ecology of these extreme environments and the future perspectives for such studies.

Temporary ponds, characterized by periodic or intermittent hydroperiods, are globally widespread in all the biogeographical regions and host peculiar biotic communities. Here we investigated shifts in diatom community assemblages across two contrasting biogeographical regions in Italy, the Mediterranean and the Alpine. The study focused on 24 temporary ponds, with 12 ponds sampled at Castelporziano (CP) and 12 at Campo Imperatore (GS). Our results highlighted that γ diversity varied significantly between the two study sites, indicating a notably greater species richness in GS compared to CP. In GS, functional richness values were generally higher, whereas no significant differences were detected for functional distance and functional divergence. Species composition differed significantly between CP and GS indicating that the two sites host distinct communities, with species turnover (0.904) which contributed most to total beta diversity (0.926), while nestedness (0.021) was negligible. CP communities were characterized by pronounced functional clustering in specific sites while GS exhibited both clustering and slight overdispersion. However, although GS communities occupy slightly larger trait space, both regions shared most functional strategies, reflecting substantial redundancy in functional traits across the two environments. Overall, diatom communities in the GS were characterized by higher frequencies of small, mobile, low-profile, and mucilaginous-tube taxa, whereas CP ponds displayed relatively higher representation of larger or motile forms. Although our study is a starting point, large-scale analyses of diatom communities are crucial, as climate change may rapidly and irreversibly alter taxonomic and functional diversity, profoundly affecting the ecology of these temporary habitats and surrounding landscapes. Graphical Abstract