Disentangling nematode-bacteria interactions using a modular soil model system and biochemical markers

Interactions between bacteria and nematode grazers are an important component of soil food webs yet, due to the cryptic habitat, they are almost exclusively investigated in artificial agar substrate. Transport, food choice and foraging experiments were performed in a modular microcosm system with the nematode Acrobeloides buetschlii and bacterial diets (Escherichia coli, Pseudomonas putida and Bacillus subtilis) in gamma-irradiated soil. Bacterial biomass was assessed by soil phospholipid fatty acids (PLFAs). Continuous random foraging of nematodes was affected by soil type. Food choice experiments revealed diet switch and time lag preference responses, suggesting that nematode population fluctuations are driven by multiple factors such as bacterial attractants, defence strategies or food quality. Application of PLFA markers revealed a strong nematode predation pressure, as biomass in P. putida declined by 50%, whereas no transport of bacteria through soil was indicated. Overall, semi-natural experimental systems are an essential prerequisite to gain a realistic picture in microbial-microfaunal interactions.

Numerical simulation of wrinkle morphology formation and the evolution of different Bacillus subtilis biofilms

Wrinkle morphology is a distinctive phenomenon observed in mature biofilms that are produced by a great number of bacteria. The wrinkle pattern depends on the mechanical properties of the agar substrate and the biofilm itself, governed by the extracellular matrix (ECM). Here we study the macroscopic structures and the evolution of Bacillus subtilis biofilm wrinkles using the commercial finite element software ABAQUS. A mechanical model and simulation are set up to analyze and evaluate bacteria biofilm's wrinkle characteristics. We uncover the wrinkle formation mechanism and enumerate the quantitative relationship between wrinkle structure and mechanical properties of biofilm and its substrate. Our work can be used to modify the wrinkle pattern and control the biofilm size.

Modeling of theBacillus subtilisBacterial Biofilm Growing on an Agar Substrate

Bacterial biofilms are organized communities composed of millions of microorganisms that accumulate on almost any kinds of surfaces. In this paper, a biofilm growth model on an agar substrate is developed based on mass conservation principles, Fick’s first law, and Monod’s kinetic reaction, by considering nutrient diffusion between biofilm and agar substrate. Our results show biofilm growth evolution characteristics such as biofilm thickness, active biomass, and nutrient concentration in the agar substrate. We quantitatively obtain biofilm growth dependence on different parameters. We provide an alternative mathematical method to describe other kinds of biofilm growth such as multiple bacterial species biofilm and also biofilm growth on various complex substrates.

Chemotaxis as an Emergent Property of a Swarm

ABSTRACT We have characterized and quantified a form of bacterial chemotaxis that manifests only as an emergent property by measuring symmetry breaking in a swarm of Myxococcus xanthus exposed to a two-dimensional nutrient gradient from within an agar substrate. M. xanthus chemotaxis requires cell-cell contact and coordinated motility, as individual motile cells exhibit only nonvectorial movement in the presence of a nutrient gradient. Genes that specifically affect M. xanthus chemotaxis include at least 10 of the 53 that express enhancer binding proteins of the NtrC-like class, an indication that this behavior is controlled through transcription, most likely by a complex signal transduction network.

Snf1 Kinases with Different β-Subunit Isoforms Play Distinct Roles in Regulating Haploid Invasive Growth

ABSTRACT The Snf1 protein kinase of Saccharomyces cerevisiae has been shown to have a role in regulating haploid invasive growth in response to glucose depletion. Cells contain three forms of the Snf1 kinase, each with a different β-subunit isoform, either Gal83, Sip1, or Sip2. We present evidence that different Snf1 kinases play distinct roles in two aspects of invasive growth, namely, adherence to the agar substrate and filamentation. The Snf1-Gal83 form of the kinase is required for adherence, whereas either Snf1-Gal83 or Snf1-Sip2 is sufficient for filamentation. Genetic evidence indicates that Snf1-Gal83 affects adherence by antagonizing Nrg1- and Nrg2-mediated repression of the FLO11 flocculin and adhesin gene. In contrast, the mechanism(s) by which Snf1-Gal83 and Snf1-Sip2 affect filamentation is independent of FLO11. Thus, the Snf1 kinase regulates invasive growth by at least two distinct mechanisms.

Antifungal Activity of Sodium Acetate and Lactobacillus rhamnosus†

The inhibition of molds by sodium acetate in deMan Rogosa Sharpe (MRS) medium, along with the antifungal activity of Lactobacillus rhamnosus VT1, was studied by the slope agar plate method. MRS agar prepared with and without sodium acetate was used as the agar substrate. A total of 42 strains of Aspergillus, Penicillium, Fusarium, Alternaria, Cladosporium, and Rhizopus were used to compare sensitivities to the inhibitory activity of sodium acetate and L. rhamnosus VT1. It was found that sodium acetate in MRS medium affected the growth of 33 of the 42 mold strains tested to various degrees. The highest sensitivity to sodium acetate was shown by strains of Fusarium, followed by strains of Penicillium, Aspergillus, and Rhizopus. L. rhamnosus VT1 also inhibited mold growth. A significant finding was that sodium acetate and L. rhamnosus VT1 in combination exhibited a possible synergistic action. Thirty-nine of the 42 mold strains tested were completely inhibited by the presence of both antifungal agents. This finding confirms that sodium acetate, a basic component of commercial MRS medium, has strong antifungal properties, and this must be taken into consideration when evaluating the antifungal activity of Lactobacillus cultures grown in MRS broth.

Proficiency Samples for Quality Assurance in Trichinella Digestion Tests

A reliable method to produce proficiency samples containing known numbers of Trichinella spiralis cysts for use in quality assurance systems for Trichinella digestion tests was developed and validated. A filtrate containing Trichinella cysts was produced by homogenizing and filtering the muscles of an experimentally infected rat. Using a stereomicroscope and micropipette, intact cysts were removed from the filtrate and were transferred onto an agar substrate to allow accurate counting and subsequent transfer into a sample matrix. The proficiency sample matrix consisted of 20-g balls of lean ground beef and was combined with 80 g of a Trichinella-free muscle tissue to obtain the required 100-g sample weight for the assay. The mean overall larval recovery from 404 proficiency samples was 93.0%. Larval recoveries ≥95, 85, and 75% occurred in 52.4, 84.4, and 94.3%, respectively, of the 404 samples tested. Results indicated that, after a short training period, technicians with no prior experience in digestion techniques performed as well as experienced technicians. The maximum shelf life of proficiency samples was not determined but was at least 3 weeks. Validation data were used to develop panels composed of proficiency samples prepared as described above and to establish guidelines for the interpretation of proficiency panel results.