Microplastic contamination is an increasing concern worldwide. Biofilms rapidly develop on surfaces in aquatic habitats, but the processes of biofilm formation and variation in bacterial community succession on different microplastics introduced into freshwater and estuarine environments are not well understood. In this study, the biofilm bacterial communities that developed on three different types of microplastics that are prevalent in the environment, high-density polyethylene (HDPE), polyethylene terephthalate (PET), and polystyrene (PS), was investigated. Virgin microplastics were incubated in microcosms over a period of 31 days with water collected along a freshwater-estuarine gradient of the Raritan River in New Jersey. Through long-read MinION sequencing of bacterial ribosomal operons, we were able to examine biofilm bacterial communities at a species- and strain-level resolution. Results indicated that both salinity level and microplastic type impacted biofilm formation and promoted colonization by distinct microbial communities. Limnobacter thiooxidans was found to be one of the most abundant microplastics colonizing-bacteria, and it is hypothesized that different types of microplastics could select for different strains. Our findings indicate that multiple groups of highly similar L. thiooxidans rRNA operons could be discerned within the community profiles. Phylogenetic reconstruction further established that various Linmobacter species uniquely colonized the different microplastics from the different sampling sites. Our findings indicate that microplastics support abundant and diverse bacterial communities and that the various types of microplastics can influence how different bacterial biofilms develop, which may have ecological impacts on aquatic ecosystems.
Cynomorium coccineum L., the desert thumb, is a rather exotic, parasitic plant unable to engage in photosynthesis, yet rich in a variety of unique compounds with a wide spectrum of biological applications. Whilst extraction, separation and isolation of such compounds is time consuming, the particular properties of the plant, such as dryness, hardness and lack of chlorophyll, render it a prime target for possible nanosizing. The entire plant, the external layer (coat) as well as its peel, are readily milled and high pressure homogenized to yield small, mostly uniform spherical particles with diameters in the range of 300 to 600 nm. The best quality of particles is obtained for the processed entire plant. Based on initial screens for biological activity, it seems that these particles are particularly active against the pathogenic fungus Candida albicans, whilst no activity could be observed against the model nematode Steinernema feltiae. This activity is particularly pronounced in the case of the external layer, whilst the peeled part does not seem to inhibit growth of C. albicans. Thanks to the ease of sample preparation, the good quality of the nanosuspension obtained, and the interesting activity of this natural product, nanosized coats of Cynomorium may well provide a lead for future development and applications as "green" materials in the field of medicine, but also environmentally, for instance in agriculture.
Current methods to characterize microbial communities generally employ sequencing of the 16S rRNA gene (< 500 bp) with high accuracy (∼ 99%) but, limited phylogenetic resolution. However, long-read sequencing now allows for the profiling of near-full length ribosomal operons [16S-ITS-23S rRNA genes] on platforms such as the Oxford Nanopore MinION. Here, we describe an rRNA operon database with >300,000 entries, representing >10,000 prokaryotic species and ∼150,000 strains. Additionally, BLAST parameters were identified for strain-level resolution using in silico mutated, mock rRNA operon sequences (70–95% identity) from four bacterial phyla and two members of the Euryarchaeota, mimicking MinION reads. MegaBLAST settings were determined that required < 3 s per read on a Mac Mini with strain-level resolution for sequences with >84% identity. These settings were tested on rRNA operon libraries generated with samples from diverse habitats: the human respiratory tract, farm/forest soils, and marine sponges (n = 1,322,818 reads for all sample sets). Most rRNA operon reads in this data set yielded best BLAST hits (95 ± 8%). However, only 38–82% of library reads were compatible with strain-level resolution, reflecting the dominance of human/biomedical associated prokaryotic entries in the database. Since the MinION and the Mac Mini are both portable, this study demonstrates the possibility of rapid strain-level microbiome analysis in the field.
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