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

Investigating degradation metabolites and underlying pathway of azo dye "Reactive Black 5" in bioaugmented floating treatment wetlands

The direct discharge of azo dyes and/or their metabolites into the environment may exert toxic, mutagenic, and carcinogenic effects on exposed fauna and flora. In this study, we analyzed the metabolites produced during the degradation of an azo dye namely Reactive Black 5 (RB5) in the bacterial-augmented floating treatment wetlands (FTWs), followed by the investigation of their underlying toxicity. To this end, a FTWs system was developed by using a common wetland plant Phragmites australis in the presence of three dye-degrading bacteria (Acinetobacter junii strain NT-15, Pseudomonas indoloxydans strain NT-38, and Rhodococcus sp. strain NT-39). We found that the FTW system effectively degraded RB5 into at least 20 different metabolites with the successful removal of color (95.5%) from the water. The fish toxicity assay revealed the nontoxic characteristics of the metabolites produced after dye degradation. Our study suggests that bacterially aided FTWs could be a suitable option for the successful degradation of azo dyes, and the results presented in this study may help improve the overall textile effluent cleanup processes.

Bioaccumulation of potentially toxic elements by submerged plants and biofilms: A critical review

The accumulation of potentially toxic elements (PTEs) in aquatic ecosystems has become a global concern, as PTEs may exert a wide range of toxicological impacts on aquatic organisms. Submerged plants and the microorganisms attached to their surfaces, however, have displayed great potential as a means of coping with such pollution. Therefore, it is crucial to understand the transport pathways of PTEs across sediment and organisms as well as their accumulation mechanisms in the presence of submerged plants and their biofilms. The majority of previous studies have demonstrated that submerged plants and their biofilms are indicators of PTE pollution in the aquatic environment, yet relatively little is known about PTE accumulation in epiphytic biofilms. In this review, we describe the transport pathways of PTEs in the aquatic environment in order to offer remarkable insights into bioaccumulation mechanisms in submerged plants and their biofilms. Based on the literature cited in this review, the roles of epiphytic biofilms in bioaccumulation and as an indicator of ecosystem health are discussed.

Accumulation of NH4 + and NO3 - inside Biofilms of Natural Microbial Consortia: Implication on Nutrients Seasonal Dynamic in Aquatic Ecosystems

Microbial biofilms are ubiquitous in aquatic ecosystems. Inside the biofilm is the nutrient-rich microenvironment promoted by the accumulation of the nutrient ions such as NH4 + and NO3 - from surrounding water. The present study investigated the characteristics of NH4 + and NO3 - accumulation into the biofilm of natural microbial consortia collected from Lake Biwa, Japan. The results showed the following: (1) the concentrations of NH4 + and NO3 - inside the biofilm were much higher than those in the surrounding water; (2) the nutrient ion concentration inside the biofilm changed in synchrony with those in the surrounding water; (3) biofilm polymers have both positively and negatively charged sites; (4) electrostatic attractive interactions between the charged sites on biofilm polymers and oppositely charged ions outside the biofilm seem to play important roles in the accumulation of nutrient ions into the biofilm from the surrounding water; (5) the bacterial community structure differs between the biofilm and surrounding water. The present study revealed that the accumulation of nutrient ions into the biofilm indicates the removal of these ions from water outside the biofilm. According to the result of this study, accumulation of ions such as NH4 + and NO3 - into the biofilm of natural microbial consortia may have implications on nutrients seasonal dynamic in aquatic ecosystems.

A comparative hierarchical analysis of bacterioplankton and biofilm metacommunity structure in an interconnected pond system

It is unknown whether bacterioplankton and biofilm communities are structured by the same ecological processes, and whether they influence each other through continuous dispersal (known as mass effects). Using a hierarchical sampling approach we compared the relative importance of ecological processes structuring the dominant fraction (relative abundance ≥0.1%) of bacterioplankton and biofilm communities from three microhabitats (open water, Nuphar and Phragmites sites) at within- and among-pond scale in a set of 14 interconnected shallow ponds. Our results demonstrate that while bacterioplankton and biofilm communities are highly distinct, a similar hierarchy of ecological processes is acting on them. For both community types, most variation in community composition was determined by pond identity and environmental variables, with no effect of space. The highest β-diversity within each community type was observed among ponds, while microhabitat type (Nuphar, Phragmites, open water) significantly influenced biofilm communities but not bacterioplankton. Mass effects among bacterioplankton and biofilm communities were not detected, as suggested by the absence of within-site covariation of biofilm and bacterioplankton communities. Both biofilm and plankton communities were thus highly structured by environmental factors (i.e., species sorting), with among-lake variation being more important than within-lake variation, whereas dispersal limitation and mass effects were not observed.

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.

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. The results also indicated that, in comparison with ion-exchange resins, ions were more loosely bound to and desorbed more easily from the biofilm polymer. This suggests that microbes in the biofilm can readily use these ions as nutrient ions. Our present findings indicate that the biofilm may play an important role in supplying nutrient ions to microbes in the biofilm and in the development of a nutrient-rich environment within the biofilm through both ion adsorption and desorption. This study shows for the first time that the inside of a biofilm can be a sustainable environment for microbes.

A great leap forward in microbial ecology

Ribosomal RNA (rRNA) sequence-based molecular techniques emerged in the late 1980s, which completely changed our general view of microbial life. Coincidentally, the Japanese Society of Microbial Ecology (JSME) was founded, and its official journal "Microbes and Environments (M&E)" was launched, in 1985. Thus, the past 25 years have been an exciting and fruitful period for M&E readers and microbiologists as demonstrated by the numerous excellent papers published in M&E. In this minireview, recent progress made in microbial ecology and related fields is summarized, with a special emphasis on 8 landmark areas; the cultivation of uncultured microbes, in situ methods for the assessment of microorganisms and their activities, biofilms, plant microbiology, chemolithotrophic bacteria in early volcanic environments, symbionts of animals and their ecology, wastewater treatment microbiology, and the biodegradation of hazardous organic compounds.

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.

Bacterial activity in plant (Schoenoplectus validus) biofilms of constructed wetlands

Biofilm-bacterial communities have been exploited in the treatment of wastewater in 'fixed-film' processes. Our understanding of biofilm dynamics requires a quantitative knowledge of bacterial growth-kinetics in these microenvironments. The aim of this paper was to apply the thymidine assay to quantify bacterial growth without disturbing the biofilm on the surfaces of emergent macrophytes (Schoenoplectus validus) of a constructed wetland. The isotope was rapidly and efficiently taken-up and incorporated into dividing biofilm-bacteria. Isotope diffusion into the biofilm did not limit the growth rate measurement. Isotope dilution was inhibited at >12 μM thymidine. Biofilm-bacterial biomass and growth rates were not correlated to the plant surface area (r(2) < 0.02). The measurements of in situ biofilm-bacterial growth rates both displayed, and accommodated, the inherent heterogeneity of the complex wetland ecosystem. Biofilm-bacterial respiratory activities, measured using the redox dye CTC, and growth rates were measured simultaneously. The dye did not interfere with bacterial growth. Biofilm-bacterial specific growth rates ranged from 1.4 ± 0.6 d(-1) to 3.3 ± 1.3 d(-1). In the constructed wetlands of this study biofilm-bacterial specific growth rates, compared to those of natural ecosystems, could be markedly improved through changes in wetland design that increased bacterial respiration while minimising biofilm growth.