抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

The microorganisms in biofilms live in a self-produced matrix of hydrated extracellular polymeric substances (EPS) that form their immediate environment. EPS are mainly polysaccharides, proteins, nucleic acids and lipids; they provide the mechanical stability of biofilms, mediate their adhesion to surfaces and form a cohesive, three-dimensional polymer network that interconnects and transiently immobilizes biofilm cells. In addition, the biofilm matrix acts as an external digestive system by keeping extracellular enzymes close to the cells, enabling them to metabolize dissolved, colloidal and solid biopolymers. Here we describe the functions, properties and constituents of the EPS matrix that make biofilms the most successful forms of life on earth.

The biofilm matrix

The rhizosphere is the interface between plant roots and soil where interactions among a myriad of microorganisms and invertebrates affect biogeochemical cycling, plant growth and tolerance to biotic and abiotic stress. The rhizosphere is intriguingly complex and dynamic, and understanding its ecology and evolution is key to enhancing plant productivity and ecosystem functioning. Novel insights into key factors and evolutionary processes shaping the rhizosphere microbiome will greatly benefit from integrating reductionist and systems-based approaches in both agricultural and natural ecosystems. Here, we discuss recent developments in rhizosphere research in relation to assessing the contribution of the micro- and macroflora to sustainable agriculture, nature conservation, the development of bio-energy crops and the mitigation of climate change.

Going back to the roots: the microbial ecology of the rhizosphere.

Nanoparticles (NPs) are increasingly used to target bacteria as an alternative to antibiotics. Nanotechnology may be particularly advantageous in treating bacterial infections. Examples include the utilization of NPs in antibacterial coatings for implantable devices and medicinal materials to prevent infection and promote wound healing, in antibiotic delivery systems to treat disease, in bacterial detection systems to generate microbial diagnostics, and in antibacterial vaccines to control bacterial infections. The antibacterial mechanisms of NPs are poorly understood, but the currently accepted mechanisms include oxidative stress induction, metal ion release, and non-oxidative mechanisms. The multiple simultaneous mechanisms of action against microbes would require multiple simultaneous gene mutations in the same bacterial cell for antibacterial resistance to develop; therefore, it is difficult for bacterial cells to become resistant to NPs. In this review, we discuss the antibacterial mechanisms of NPs against bacteria and the factors that are involved. The limitations of current research are also discussed.

/pdf/the-antimicrobial-activity-of-nanoparticles-present-455xafgyws.pdf

The antimicrobial activity of nanoparticles: present situation and prospects for the future

Plants host distinct bacterial communities on and inside various plant organs, of which those associated with roots and the leaf surface are best characterized. The phylogenetic composition of these communities is defined by relatively few bacterial phyla, including Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. A synthesis of available data suggests a two-step selection process by which the bacterial microbiota of roots is differentiated from the surrounding soil biome. Rhizodeposition appears to fuel an initial substrate-driven community shift in the rhizosphere, which converges with host genotype–dependent finetuning of microbiota profiles in the selection of root endophyte assemblages. Substrate-driven selection also underlies the establishment of phyllosphere communities but takes place solely at the immediate leaf surface. Both the leaf and root microbiota contain bacteria that provide indirect pathogen protection, but root microbiota members appear to serve additional host functions through the acquisition of nutrients from soil for plant growth. Thus, the plant microbiota emerges as a fundamental trait that includes mutualism enabled through diverse biochemical mechanisms, as revealed by studies on plant growth–promoting and plant health–promoting bacteria.

Structure and functions of the bacterial microbiota of plants

Bacteria form communities known as biofilms, which disassemble over time. In our studies outlined here, we found that, before biofilm disassembly, Bacillus subtilis produced a factor that prevented biofilm formation and could break down existing biofilms. The factor was shown to be a mixture of D-leucine, D-methionine, D-tyrosine, and D-tryptophan that could act at nanomolar concentrations. D-amino acid treatment caused the release of amyloid fibers that linked cells in the biofilm together. Mutants able to form biofilms in the presence of D-amino acids contained alterations in a protein (YqxM) required for the formation and anchoring of the fibers to the cell. D-amino acids also prevented biofilm formation by Staphylococcus aureus and Pseudomonas aeruginosa. D-amino acids are produced by many bacteria and, thus, may be a widespread signal for biofilm disassembly.

/pdf/d-amino-acids-trigger-biofilm-disassembly-3zd7io0dgh.pdf

D-amino acids trigger biofilm disassembly.

Bacillus subtilis forms biofilms whose constituent cells are held together by an extracellular matrix. Previous studies have shown that the protein TasA and an exopolysaccharide are the main components of the matrix. Given the importance of TasA in biofilm formation, we characterized the physicochemical properties of this protein. We report that purified TasA forms fibers of variable length and 10–15 nm in width. Biochemical analyses, in combination with the use of specific dyes and microscopic analyses, indicate that TasA forms amyloid fibers. Consistent with this hypothesis, TasA fibers required harsh treatments (e.g., formic acid) to be depolymerized. When added to a culture of a tasA mutant, purified TasA restored wild-type biofilm morphology, indicating that the purified protein retained biological activity. We propose that TasA forms amyloid fibers that bind cells together in the biofilm.

https://www.pnas.org/content/pnas/107/5/2230.full.pdf

Amyloid fibers provide structural integrity to Bacillus subtilis biofilms.

Podosphaera fusca is the main causal agent of cucurbit powdery mildew in Spain. Four Bacillus subtilis strains, UMAF6614, UMAF6619, UMAF6639, and UMAF8561, with proven ability to suppress the disea...

/pdf/the-iturin-and-fengycin-families-of-lipopeptides-are-key-1jj8stdvlv.pdf

The iturin and fengycin families of lipopeptides are key factors in antagonism of Bacillus subtilis toward Podosphaera fusca

Plant protection and growth stimulation by microorganisms: biotechnological applications of Bacilli in agriculture

Antibiotics have been extensively used in the treatment of infectious diseases The lethality of these compounds has been exploited in clinical and laboratory approaches and their specific targets in bacterial physiology elucidated However, along with this development of drugs has come the problem of increasing resistance in microbes, resulting in dramatically reduced therapeutic effectiveness 1 Pathogenic microbes have rapidly evolved efficient mechanisms of resistance, including increased efflux, enzymatic inactivation, target modification, or biofilm formation 2

The concentrations of these molecules required to achieve an antimicrobial effect are likely extremely high compared to the concentrations in which these molecules can be found in natural environments While we know their effect at lethal concentrations, the activities of these molecules at concentrations below the inhibitory limit needs deeper investigation 3 The findings of the nineteenth-century pharmacologist Hugo Schulz, who noted that certain disinfectants could have stimulatory effect on yeast growth at low concentrations, could be considered the first evidence that the action of an antimicrobial can cause a differential response depending on the concentration His observation was the first example of what it would be later called hormesis This term was coined by Chester Southam and John Ehrlich in the mid-1920s and it is used to refer to the ability of certain molecules to induce diverse responses depending on the concentration used 3 The vast amount of information related to the lethal concentration of antibiotics, targets, or side effects, contrasts dramatically with the relatively few studies focused on their effect at concentrations below the MIC (minimal inhibitory concentration) As pointed by Davies, only a small fraction of natural products that have antimicrobial activity have been extensively studied, and their role in natural settings is poorly understood Thus it is possible that many of these molecules formerly considered antibiotics might have a different function in nature It is now believed that many of these compounds might act as signaling molecules that modulate gene expression in microbial populations, or physiological functions such as motility, pigmentation, and production of metabolites, and thus facilitate inter- and intra-species communication 4

This fundamental lack of understanding may be rooted in our conception of the microbial world as single and separated species, as they are usually studied under laboratory conditions However, in nature, each niche is complex, and to different extents, variable in microbial community composition 5,6–8 Therefore it is conceivable that molecules fluctuate in concentration and diversity, thus facilitating communication among species 9 Many interesting lines of research are currently focused on understanding how some antibiotics may affect, either positively or negatively, cell-cell communication systems, and the physiological responses that are affected as a result In some cases, natural products can influence the ability of bacteria to transition from a planktonic state to complex multicellular aggregates attached to surfaces known as biofilms Cells in bioflms are encased in an extracellular matrix which can serve as a barrier for antibiotics 10 One example is the biofilm produced by the gram-negative pathogen, Pseudomonas aeruginosa, which is resistant to antibiotics produced by gram-positive competitors 11 Studies on many model microorganisms from the genera Bacillus, Streptomyces, and Pseudomonas are shedding new light on the fascinating world of cell signaling and communication in microbial world 5,12,13

We will discuss in this review several examples of the dual functions of some well-known antibiotics, including those that when used at sub-inhibitory concentrations (SIC) promote an interesting response in bacterial populations and the ecological implications of such varied responses Also, the role of other naturally synthesized antibiotics will be discussed in the context of cell communication in natural environments, including one of the most exploited environmental niches for antibiotic discovery, the soil

Diego Romero

Papers

D-amino acids trigger biofilm disassembly.

Amyloid fibers provide structural integrity to Bacillus subtilis biofilms.

The iturin and fengycin families of lipopeptides are key factors in antagonism of Bacillus subtilis toward Podosphaera fusca

Plant protection and growth stimulation by microorganisms: biotechnological applications of Bacilli in agriculture

Antibiotics as Signal Molecules