Analysis of Dissolved Organic Nutrients in the Interstitial Water of Natural Biofilms.

In biofilms, the matrix of extracellular polymeric substances (EPSs) retains water in the interstitial region of the EPS. This interstitial water is the ambient environment for microorganisms in the biofilms. The nutrient condition in the interstitial water may affect microbial activity in the biofilms.

Characterization of the internal ion environment of biofilms based on charge density and shape of ion.

Biofilm polymers contain both electrically positively and negatively charged sites. These charged sites enable the biofilm to trap and retain ions leading to an important role of biofilm such as nutrient recycling and pollutant purification. Much work has focused on the ion-exchange capacity of biofilms, and they are known to adsorb ions through an exchange mechanism between the ions in solution and the ions adsorbed to the charged sites on the biofilm polymer.

Virtual metagenome reconstruction from 16S rRNA gene sequences.

Microbial ecologists have investigated roles of species richness and diversity in a wide variety of ecosystems. Recently, metagenomics have been developed to measure functions in ecosystems, but this approach is cost-intensive. Here we describe a novel method for the rapid and efficient reconstruction of a virtual metagenome in environmental microbial communities without using large-scale genomic sequencing.

Analysis of the ion adsorption-desorption characteristics of biofilm matrices.

The characteristics of biofilm polymers formed on stone surfaces in Lake Biwa and ion adsorption and desorption to and from these biofilms were investigated. The results indicated that both positively and negatively charged sites exist in the biofilm polymer. A physicochemical interaction between these sites and ions in the surrounding water seems to promote the adsorption of ions to the biofilm through an attractive electrostatic interaction and an ion-exchange mechanism.

Seasonal change of bacterial community structure in a biofilm formed on the surface of the aquatic macrophyte Phragmites australis.

The seasonal change of bacterial community structure in biofilms on the surface of reed (Phragmites australis) was investigated for about three years (from 2005 June to 2008 March) in Lake Biwa by comparing it with that in surrounding lake water. The community structure in biofilms was different from that in the lake water throughout the seasons and years. The community structure in lake water was similar in the same seasons of different years, corresponding to similar environmental factors (i.

Direct observation and analysis of bacterial growth on an antimicrobial surface.

Cells of Escherichia coli NBRC 3972 and Staphylococcus aureus NBRC 12732 were inoculated onto an agar (1.5%) medium varying in nutrient concentration from full strength of the nutrient broth (NB) to 1/10 NB. Immediately thereafter, the inoculated agar was placed on antimicrobial and nonantimicrobial surfaces in such a way that the microbial cells came into contact with these surfaces.

Bacterial attachment over a wide range of ionic strengths.

The number of bacterial cells adhered on a glass surface was counted over a wide range of ionic strengths. The counted number increased linearly with the square root of time. The rate of attachment increased with the increase in ionic strength and then plateaued.

Analysis of How a Biofilm Forms on the Surface of the Aquatic Macrophyte Phragmites australis.

The process by which a biofilm forms on the surface of the aquatic macrophyte Phragmites australis was investigated over a period of about two months (from mid-May to late-July, 2008) in Lake Biwa. The biofilm formed relatively quickly, its wet weight per unit area after seven day being that of a mature biofilm. This speed can be attributed to the many active bacteria in the early stage of its formation and the extracellular polymeric substances (EPS) they produce.

Rice seeds as sources of endophytic bacteria.

Endophytic bacteria are considered to originate from the external environment. To examine the hypothesis that rice (Oryza sativa, cultivar Kinuhikari) seeds are a source of endophytic bacteria, we isolated endophytic bacteria from the shoots, remains of the seeds, and roots of rice seedlings that were aseptically cultivated in vitro from surface-disinfected seeds. Of the various bacterial strains isolated, the closest relatives, identified by 16S rRNA gene sequencing, were: Bacillus firmus, B.

Nutrient-rich microhabitats within biofilms are synchronized with the external environment.

The nutrient ion concentrations in the interstitial waters of biofilms (BFs) formed on reed and stone surfaces were investigated in the northern and southern basins of Lake Biwa over several years. The following were observed for both types of BF: 1) Concentrations of ammonium, nitrate, nitrite, and phosphate ions were much (hundreds to thousands of times) higher in the BFs than in the surrounding lake water; 2) the concentration of ions, especially nitrate ions, in the BFs changed seasonally, being higher from winter to spring and lower from summer to autumn, synchronizing with the changes in the lake water; 3) dissolved-form N:P ratios were higher in the lake water than BFs; and 4) the bacterial flora of the BFs differed from that of the lake water, with smaller seasonal variations. The present study reveals for the first time that the inside of BFs in a natural environment is rich in nutrient ions and shows similar seasonal changes as the lake water.

Cloth colorization caused by microbial biofilm.

In this study, cloth disfeaturement was investigated biologically. To clarify whether or not microbes can cause cloth disfeaturement, and to identify the microbes causing the disfeaturement, worn cloth samples were incubated on sweat-ingredient agar medium. Non-sterilized cloth samples became yellow-colored during incubation, and bacterial strains belonging to the genera Bacillus, Brevibacterium, Kocuria, Micrococcus and Staphylococcus were isolated from the yellow-colored parts.

Endophytic bacteria in the rice plant.

Endophytic bacteria are defined as bacteria detected inside surface-sterilized plants or extracted from inside plants and having no visibly harmful effects on the plants. Various kinds of endophytic bacteria, such as Pantoea, Methylobacterium, Azospirillum, Herbaspirillum, Burkholderia and Rhizobium etc., have been found inside rice plants.

Electrophoretic mobility of Bacillus subtilis knockout mutants with and without flagella.

Mutants of Bacillus subtilis 168 strain were obtained by inactivation of a specific gene by homologous recombination with the plasmid pMutinT3. The cell surface properties of these strains were characterized by measuring the electrophoretic mobility of the cells as a function of pH and ionic strength. The surface properties were different for the strains possessing flagella on their cells and strain FlgB, having no flagellum, due to knockout of the corresponding gene.