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. In the present study, we measured the concentrations of dissolved organic nutrients, i.e., saccharides and proteins, contained in the interstitial water of biofilms formed on the stones. We also analyzed the molecular weight distribution, chemical species, and availability to bacteria of some saccharides in the interstitial water. Colorimetric assays showed that the concentrations of saccharides and proteins in the biofilm interstitial water were significantly higher (ca. 750 times) than those in the surrounding lake waters (p < 0.05). Chromatographic analyses demonstrated that the saccharides in the interstitial waters were mainly of low molecular-weight saccharides such as glucose and maltose, while proteins in the interstitial water were high molecular-weight proteins (over 7000 Da). Bacterial growth and production of EPS occurred simultaneously with the decrease in the low molecular-weight saccharide concentrations when a small portion of biofilm suspension was inoculated to the collected interstitial water, suggesting that the dissolved saccharides in the interstitial water support bacterial growth and formation of biofilms.

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. We demonstrate this approach using 16S rRNA gene sequences obtained from denaturing gradient gel electrophoresis analysis, mapped to fully sequenced genomes, to reconstruct virtual metagenome-like organizations. Furthermore, we validate a virtual metagenome using a published metagenome for cocoa bean fermentation samples, and show that metagenomes reconstructed from biofilm formation samples allow for the study of the gene pool dynamics that are necessary for biofilm growth.

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.e., temperature, dissolved oxygen, and light intensity) and nutrient ion concentrations at the same season. However, the community structure in the biofilms was not similar in the same season of different years. This seems to be due to the formation of new biofilms on sprouted reeds in every early summer and the high nutrient concentrations and bacterial density in subsequently formed biofilms. Although the community structure in the biofilms changed along with the seasonal change, the bacteria belonging to Bacillus and Paenibacillus were detected in any season. This study revealed the possibility that the bacterial community structure in the initial stage of the biofilm formation govern the subsequent seasonal change of the community structure in biofilms.