Characterization of the Bacterial Biofilm Communities Present in Reverse-Osmosis Water Systems for Haemodialysis

A laboratory ice machine as a cold oligotrophic artificial microbial niche for biodiscovery

Microorganisms are ubiquitously distributed in nature and usually appear as biofilms attached to a variety of surfaces. Here, we report the development of a thick biofilm in the drain pipe of several standard laboratory ice machines, and we describe and characterise, through culture-dependent and -independent techniques, the composition of this oligotrophic microbial community. By using culturomics, 25 different microbial strains were isolated and taxonomically identified. The 16S rRNA high-throughput sequencing analysis revealed that Bacteroidota and Proteobacteria were the most abundant bacterial phyla in the sample, followed by Acidobacteriota and Planctomycetota, while ITS high-throughput sequencing uncovered the fungal community was clearly dominated by the presence of a yet-unidentified genus from the Didymellaceae family. Alpha and beta diversity comparisons of the ice machine microbial community against that of other similar cold oligotrophic and/or artificial environments revealed a low similarity between samples, highlighting the ice machine could be considered a cold and oligotrophic niche with a unique selective pressure for colonisation of particular microorganisms. The recovery and analysis of high-quality metagenome-assembled genomes (MAGs) yielded a strikingly high rate of new species. The functional profiling of the metagenome sequences uncovered the presence of proteins involved in extracellular polymeric substance (EPS) and fimbriae biosynthesis and also allowed us to detect the key proteins involved in the cold adaptation mechanisms and oligotrophic metabolic pathways. The metabolic functions in the recovered MAGs confirmed that all MAGs have the genes involved in psychrophilic protein biosynthesis. In addition, the highest number of genes for EPS biosynthesis was presented in MAGs associated with the genus Sphingomonas, which was also recovered by culture-based method. Further, the MAGs with the highest potential gene number for oligotrophic protein production were closely affiliated with the genera Chryseoglobus and Mycobacterium. Our results reveal the surprising potential of a cold oligotrophic microecosystem within a machine as a source of new microbial taxa and provide the scientific community with clues about which microorganisms are able to colonise this ecological niche and what physiological mechanisms they develop. These results pave the way to understand how and why certain microorganisms can colonise similar anthropogenic environments.

A case study of environmental pollution by pathogenic bacteria and metal(oid)s at Soran Landfill Site, Erbil, Iraqi Kurdistan Region

Environmental pollution is a serious issue all around the world, especially when it is caused by metal(oid)s and pathogenic microorganisms. This study reports here for the first time on the contamination of soil and water with metal(oid)s and pathogenic bacteria directly resulting from the Soran Landfill Site. Soran landfill is a level 2 solid waste disposal site that lacks leachate collection infrastructure. The site is potentially an environmental and public hazard caused by metal(oid)s content and significantly dangerous pathogenic microorganisms through leachate release into the soil and nearby river. This study reports on the levels of the metal(oid)s content of As, Cd, Co, Cr, Cu, Mn, Mo, Pb, Zn, and Ni obtained by inductively coupled plasma mass spectrometer in soil, leachate stream mud, and leachate samples. Five pollution indices are used to assess potential environmental risks. According to the indices, Cd and Pb contamination is significant, whereas As, Cu, Mn, Mo, and Zn pollution is moderate. A total of 32 isolates of bacteria were defined from soil, leachate stream mud, and liquid leachate samples: 18, 9, and 5, respectively. Moreover, 16 s rRNA analysis suggested that the isolates belong to three enteric bacterial phyla of Proteobacteria, Actinobacteria, and Firmicutes. The closest GenBank matches of 16S rDNA sequences indicated the presence of the genera: Pseudomonas, Bacillus, Lysinibacillus, Exiguobacterium, Trichococcus, Providencia, Enterococcus, Macrococcus, Serratia, Salinicoccus, Proteus, Rhodococcus, Brevibacterium, Shigella, Micrococcus, Morganella, Corynebacterium, Escherichia, and Acinetobacter. The identity percentage was mostly between 95%-100%. The results of this study show the levels of microbiological and geochemical contamination of soils, surface and potentially ground water with harmful microorganisms and toxic metal(oid)s originating specifically from Soran landfill leachate which subsequently incorporated into the surrounding environment, creating thus a considerable health and environmental risk.

Biofouling of reverse osmosis membranes: assessment by surface-enhanced Raman spectroscopy and microscopic imaging

The decline in the performance of spiral-wound reverse osmosis (SWRO) membranes is frequently due to biofouling. This study focus on qualitative and quantitative diagnosis of SWRO membrane biofouling. Bacterial counts on the different surfaces of the fouled membranes were carried out. Surface enhanced Raman spectroscopy (SERS) was performed to highlight clogging materials as well as their natures and identity. The topography of the fouled membranes and the structures of biofilms were visualized by fluorescence microscopy (FM) and scanning electron microscopy (SEM). The results indicated the presence of bacteria in the different SWRO membrane areas. Those strongly adhered were significantly higher than those weakly. It varied between 26 × 10⁵ and 262 × 10⁵ CFU m^-2. However, SERS mapping showed different fouling levels and the thickness of the fouling layer was 5 µm. Microscopic imaging revealed biotic and abiotic deposits. These data can together allow better management of the seawater desalination process.

Gastrointestinal Microbiota and Parasite-Fauna of Wild Dissostichus eleginoides Smitt, 1898 Captured at the South-Central Coast of Chile

Dissotichus eleginoides has a discontinuous circumpolar geographic distribution restricted to mountains and platforms, mainly in Subantarctic and Antarctic waters of the southern hemisphere, including the Southeast Pacific, Atlantic and Indian oceans and in areas surrounding the peninsular platforms of subantarctic islands. The aim of this work was to determine and characterize the gastrointestinal parasitic and microbial fauna of specimens of D. eleginoides captured in waters of the south-central zone of Chile. The magnitude of parasitism in D. eleginoides captured in waters of the south-central zone of Chile is variable, and the parasite richness is different from that reported in specimens from subantarctic environments. Next-generation sequencing (NGS) of the microbial community associated to intestine showed a high diversity, where Proteobacteria, Firmicutes, and Bacteriodetes were the dominant phyla. However, both parasitic and microbial structures can vary between fish from different geographic regions

Characterization of Arsenite-Oxidizing Bacteria Isolated from Arsenic-Rich Sediments, Atacama Desert, Chile

Arsenic (As), a semimetal toxic for humans, is commonly associated with serious health problems. The most common form of massive and chronic exposure to As is through consumption of contaminated drinking water. This study aimed to isolate an As resistant bacterial strain to characterize its ability to oxidize As (III) when immobilized in an activated carbon batch bioreactor and to evaluate its potential to be used in biological treatments to remediate As contaminated waters. The diversity of bacterial communities from sediments of the As-rich Camarones River, Atacama Desert, Chile, was evaluated by Illumina sequencing. Dominant taxonomic groups (>1%) isolated were affiliated with Proteobacteria and Firmicutes. A high As-resistant bacterium was selected (Pseudomonas migulae VC-19 strain) and the presence of aio gene in it was investigated. Arsenite detoxification activity by this bacterial strain was determined by HPLC/HG/AAS. Particularly when immobilized on activated carbon, P. migulae VC-19 showed high rates of As(III) conversion (100% oxidized after 36 h of incubation). To the best of our knowledge, this is the first report of a P. migulae arsenite oxidizing strain that is promising for biotechnological application in the treatment of arsenic contaminated waters.