The evolution of bacterial pathogens in the Anthropocene

The overlooked evolutionary dynamics of 16S rRNA revises its role as the "gold standard" for bacterial species identification

The role of 16S rRNA has been and largely remains crucial for the identification of microbial organisms. Although 16S rRNA could certainly be described as one of the most studied sequences ever, the current view of it remains somewhat ambiguous. While some consider 16S rRNA to be a variable marker with resolution power down to the strain level, others consider them to be living fossils that carry information about the origin of domains of cellular life. We show that 16S rRNA is clearly an evolutionarily very rigid sequence, making it a largely unique and irreplaceable marker, but its applicability beyond the genus level is highly limited. Interestingly, it seems that the evolutionary rigidity is not driven by functional constraints of the sequence (RNA-protein interactions), but rather results from the characteristics of the host organism. Our results suggest that, at least in some lineages, Horizontal Gene Transfer (HGT) within genera plays an important role for the evolutionary non-dynamics (stasis) of 16S rRNA. Such genera exhibit an apparent lack of diversification at the 16S rRNA level in comparison to the rest of a genome. However, why it is limited specifically and solely to 16S rRNA remains enigmatic.

Marine diseases and the Anthropocene: Understanding microbial pathogenesis in a rapidly changing world

Healthy marine ecosystems are paramount for Earth's biodiversity and are key to sustaining the global economy and human health. The effects of anthropogenic activity represent a pervasive threat to the productivity of marine ecosystems, with intensifying environmental stressors such as climate change and pollution driving the occurrence and severity of microbial diseases that can devastate marine ecosystems and jeopardise food security. Despite the potentially catastrophic outcomes of marine diseases, our understanding of host-pathogen interactions remains an understudied aspect of both microbiology and environmental research, especially when compared to the depth of information available for human and agricultural systems. Here, we identify three avenues of research in which we can advance our understanding of marine disease in the context of global change, and make positive steps towards safeguarding marine communities for future generations.

Plastic-microbe interaction in the marine environment: Research methods and opportunities

Approximately 9 million metric tons of plastics enters the ocean annually, and once in the marine environment, plastic surfaces can be quickly colonised by marine microorganisms, forming a biofilm. Studies on plastic debris-biofilm associations, known as plastisphere, have increased exponentially within the last few years. In this review, we first briefly summarise methods and techniques used in exploring plastic-microbe interactions. Then we highlight research gaps and provide future research opportunities for marine plastisphere studies, especially, on plastic characterisation and standardised biodegradation tests, the fate of "environmentally friendly" plastics, and plastisphere of coastal habitats. Located in the tropics, Southeast Asian (SEA) countries are significant contributors to marine plastic debris. However, plastisphere studies in this region are lacking and therefore, we discuss how the unique environmental conditions in the SEA seas may affect plastic-microbe interaction and why there is an imperative need to conduct plastisphere studies in SEA marine environments. Finally, we also highlight the lack of understanding of the pathogenicity and ecotoxicological effects of plastisphere on marine ecosystems.

Bacterial colonisation dynamics of household plastics in a coastal environment

Accumulation of plastics in the marine environment has widespread detrimental consequences for ecosystems and wildlife. Marine plastics are rapidly colonised by a wide diversity of bacteria, including human pathogens, posing potential risks to health. Here, we investigate the effect of polymer type, residence time and estuarine location on bacterial colonisation of common household plastics, including pathogenic bacteria. We submerged five main household plastic types: low-density PE (LDPE), high-density PE (HDPE), polypropylene (PP), polyvinyl chloride (PVC) and polyethylene terephthalate (PET) at an estuarine site in Cornwall (U.K.) and tracked bacterial colonisation dynamics. Using both culture-dependent and culture-independent approaches, we found that bacteria rapidly colonised plastics irrespective of polymer type, reaching culturable densities of up to 1000 cells cm³ after 7 weeks. Community composition of the biofilms changed over time, but not among polymer types. The presence of pathogenic bacteria, quantified using the insect model Galleria mellonella, increased dramatically over a five-week period, with Galleria mortality increasing from 4% in week one to 65% in week five. No consistent differences in virulence were observed between polymer types. Pathogens isolated from plastic biofilms using Galleria enrichment included Serratia and Enterococcus species and they harboured a wide range of antimicrobial resistance genes. Our findings show that plastics in coastal waters are rapidly colonised by a wide diversity of bacteria independent of polymer type. Further, our results show that marine plastic biofilms become increasingly associated with virulent bacteria over time.

Reciprocal interactions between anthropogenic stressors and insect microbiota

Insects play many important roles in nature due to their diversity, ecological role, and impact on agriculture or human health. They are directly influenced by environmental changes and in particular anthropic activities that constitute an important driver of change in the environmental characteristics. Insects face numerous anthropogenic stressors and have evolved various detoxication mechanisms to survive and/or resist to these compounds. Recent studies highligted the pressure exerted by xenobiotics on insect life-cycle and the important role of insect-associated bacterial microbiota in the insect responses to environmental changes. Stressor exposure can have various impacts on the composition and structure of insect microbiota that in turn may influence insect biology. Moreover, bacterial communities associated with insects can be directly or indirectly involved in detoxification processes with the selection of certain microorganisms capable of degrading xenobiotics. Further studies are needed to assess the role of insect-associated microbiota as key contributor to the xenobiotic metabolism and thus as a driver for insect adaptation to polluted habitats.

Laboratory Plasticware Induces Expression of a Bacterial Virulence Factor

Pollution with microplastic has become a prime environmental concern. The various ways in which human-made polymers and microorganisms interact are little understood, and this is particularly true for microplastic and pathogenic microorganisms. Previous reports demonstrated that expression of central virulence-associated protein A (VapA) of the pathogenic bacterium Rhodococcus equi is shut off at 30°C, whereas it is strongly expressed at 37°C, a temperature which may serve as an intrahost cue. Here, we show that cultivation at 30°C in disposable plastic tubes increases mRNA levels of vapA 70-fold compared to growth in conventional glass tubes. Strong expression of vapA in plastic tubes does not seem to be caused by a compound leaching from plastic but rather by tube surface properties. Expression stimulation during growth in plastic is regulated by the R. equi transcription regulators VirR and VirS, indicating that plastic-induced vapA expression is (co)regulated through the canonical vapA expression pathway. Our observations have important implications for the future analysis and assessment of environmental microplastic contaminations in that they show that, in principle, contact of pathogens with environmental plastic can increase their virulence.

IMPORTANCE Millions of tons small plastic pieces (microplastic) find their way into the environment every year. They pose digestive and toxicity problems to various life forms in soil, freshwater, and seawater. Additionally, microplastic offers an opportunity for microorganisms to attach and to become an important part of a “plastisphere community.” The significance of our study lies in the documentation of a sharp increase in production of a central virulence factor by a bacterial pathogen when the bacterium is in touch with certain makes of plastic. Although this feature may not reflect an increased health risk in case of this particular soilborne pathogen, our data disclose a new facet of how microplastics can endanger life.

Sewage-associated plastic waste washed up on beaches can act as a reservoir for faecal bacteria, potential human pathogens, and genes for antimicrobial resistance

Sewage-associated plastic wastes, such as wet wipes and cotton bud sticks, commonly wash up on beaches; however, it is unclear whether this represents a public health risk. In this study, sewage-associated plastic waste, and naturally occurring substrates (seaweed and sand), were collected from ten beaches along the Firth of Forth estuary (Scotland, UK) and analysed using selective media for the faecal indicator organisms (FIOs) E. coli and intestinal enterococci (IE), and potential human pathogens (Vibrio spp.). Minimum inhibitory concentration (MIC) analysis was used to determine antibiotic resistance in selected strains. FIOs and Vibrio were more often associated with wet wipes and cotton bud sticks than with seaweed, and there was evidence of resistance to several antibiotics. This work demonstrates that plastics associated with sewage pollution can facilitate the survival and dissemination of FIOs and Vibrio and thus, could present an as yet unquantified potential risk to human health at the beach.

Antimicrobial resistance acquisition via natural transformation: context is everything

Natural transformation is a process where bacterial cells actively take up free DNA from the environment and recombine it into their genome or reconvert it into extra-chromosomal genetic elements. Although this mechanism is known to mediate the uptake of antibiotic resistance determinants in a range of human pathogens, its importance in the spread of antimicrobial resistance is not always appreciated. This review highlights the context in which transformation takes place: in diverse microbiomes, in interaction with other forms of horizontal gene transfer and in increasingly polluted environments. This examination of the abiotic and biotic drivers of transformation reveals that it could be more important in the dissemination of resistance genes than is often recognised.

The Proposal and Necessity of the Numerical Description of Nano- and Microplastics' Surfaces (Plastisphere)

The constantly growing amount of synthetic materials < 5 mm, called microplastics (MPs), is fragmented in the environment. Thus, their surface, Plastisphere, is substantially increasing forming an entirely new ecological niche. It has already been extensively studied by microbiologists observing the biofilm and by material scientists interested in the weathering of polymer materials. This paper aims to construct a bridge between the physical and chemical description of the Plastisphere and its microbiological and ecological significance. Various algorithms, based on the analysis of pictures obtained by scanning electron microscopy (SEM), are proposed to describe in detail the morphology of naturally weathered polymers. In particular, one can study the size and distribution of fibres in a standard filter, search the synthetic debris for mapping, estimate the grain size distribution, quantitatively characterize the different patterns of degradation for polymer spheres and ghost nets, or calculate the number of pores per surface. The description and visualization of a texture, as well as the classification of different morphologies present on a surface, are indispensable for the comprehensive characterization of weathered polymers found inside animals (e.g., fishes). All these approaches are presented as case studies and discussed within this work.