Isolation of effective 3-chlorobenzoate-degraders in soil using community analyses by PCR-DGGE

Effects of Land Use Changes from Paddy Fields on Soil Bacterial Communities in a Hilly and Mountainous Area

Soil bacterial community structures in terraced rice fields and abandoned lands in a hilly and mountainous area were analyzed using 16S rRNA gene sequences. The DGGE band patterns of each soil were similar. Based on pyrosequencing data, the richness and diversity of bacterial species were slightly higher in paddy fields than in other soils. A beta-diversity analysis clearly indicated that the bacterial community structure in paddy fields differed from those in non-paddy field lands and crop fields that had not been used as a paddy field. These results may reflect the history of land use.

Comparison among amoA primers suited for quantification and diversity analyses of ammonia-oxidizing bacteria in soil

Ammonia monooxygenase subunit A gene (amoA) is frequently used as a functional gene marker for diversity analysis of ammonia-oxidizing bacteria (AOB). To select a suitable amoA primer for real-time PCR and PCR-denaturing gradient gel electrophoresis (DGGE), three reverse primers (degenerate primer amoA-2R; non-degenerate primers amoA-2R-GG and amoA-2IR) were examined. No significant differences were observed among the three primers in terms of quantitative values of amoA from environmental samples using real-time PCR. We found that PCR-DGGE analysis with the amoA-2IR primer gave the best results in this studied soil. These results indicate that amoA-2IR is a suitable primer for community analysis of AOB in the environment.

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.

Soil clone library analyses to evaluate specificity and selectivity of PCR primers targeting fungal 18S rDNA for denaturing-gradient gel electrophoresis (DGGE)

We evaluated the fungal specificity and detection bias of four fungal 18S rRNA gene (18S rDNA) primer sets for denaturing-gradient gel electrophoresis (DGGE). We constructed and compared clone libraries amplified from upland and paddy field soils with each primer set (1, NS1/GCFung; 2, FF390/FR1-GC; 3, NS1/FR1-GC; and 4, NS1/EF3 for the first PCR and NS1/FR1-GC for the second PCR). Primer set 4 (for nested PCR) showed the highest specificity for fungi but biased specific sequences. Sets 1, 2, and 3 (for single PCR) amplified non-fungal eukaryotic sequences (from 7 to 16% for upland soil and from 20 to 31% for paddy field soil) and produced libraries with similar distributions of fungal 18S rDNA sequences at both the phylum and the class level. Set 2 tended to amplify more diverse fungal sequences, maintaining higher specificity for fungi. In addition, clone analyses revealed differences among primer sets in the frequency of chimeras. In upland field soil, the libraries amplified with primer sets 3 and 4, which targeted long fragments, contained many chimeric 18S rDNA sequences (18% and 48%, respectively), while the libraries obtained with sets 1 and 2, which targeted short fragments, contained fewer chimeras (5% and 10%, respectively).

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. The BFs in an aquatic environment provide a microenvironment capable of sustaining a specific bacterial flora different from that in the surrounding lake water.

High expression levels of chitinase genes in Streptomyces coelicolor A3(2) grown in soil

Although Streptomyces species are major chitin-degraders in soil ecosystems, the expression of the diverse chitinase genes within Streptomyces coelicolor grown in soil has not been assessed. As a first step, the induction pattern of nine chitinase genes in S. coelicolor growing in autoclaved soil was compared with those in liquid cultures. The relative expression levels of nine chitinase genes were measured using real-time reverse transcription PCR. The expression of all chitinase genes was induced by chitin in both autoclaved soil and liquid cultures, but to different levels. The expression levels of five chitinase genes in autoclaved soil were significantly higher than those in the liquid cultures. In particular, a putative chitinase gene, chitinase H, showed the highest induction in autoclaved soil. The same induction pattern was confirmed in nonautoclaved soil, indicating that soil contains some factors affecting the expression of chitinase genes. The chiH gene product, ChiH, cloned in Streptomycetes lividans was secreted and exhibited chitin degradation activity that was stable within a wide range of acidic pHs. The disruption of dasR, a transcriptional regulator for the uptake of N-acetylglucosamine, abolished the expression of chiH, demonstrating that DasR is required for the regulation of ChiH expression.

Suppressed-priming PCR, a novel concept of DNA quantification based on PCR kinetics

The concept of an unbiased DNA quantification method is proposed based on PCR kinetics. A set of PCRs was performed with a dilution series of primers, which differently limited DNA amplification. The difference in amplification efficiency between the DNA templates reflected the estimates of their relative amounts. This concept might serve as a theoretical base for further development of accurate and robust PCR-based quantification methods.

A new approach to retrieve full lengths of functional genes from soil by PCR-DGGE and metagenome walking

Metagenomes are a vast genetic resource, and various approaches have been developed to explore them. Here, we present a new approach to retrieve full lengths of functional genes from soil DNA using PCR-denaturing gradient gel electrophoresis (DGGE) followed by metagenome walking. Partial fragments of benzoate 1,2-dioxygenase alpha subunit gene (benA) were detected from a 3-chlorobenzoate (3CB)-dosed soil by PCR-DGGE, and one DGGE band induced by 3CB was used as a target fragment for metagenome walking. The walking retrieved the flanking regions of the target fragment from the soil DNA, resulting in recovery of the full length of benA and also downstream gene (benB). The same strategy retrieved another gene, tfdC, and a complete tfdC and two downstream genes were obtained from the same soil. PCR-DGGE allows screening for target genes based on their potential for degrading contaminants in the environment. This feature provides an advantage over other existing metagenomic approaches.

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. The EPS carried electric charges that attracted nutrient ions from surrounding lake water, which, by electrostatic interaction, reached a high concentration as early as day 7 of the formation process. This significantly affected the biofilm community, which differed greatly from that of the lake water even at the beginning of biofilm formation. Brown amorphous compounds (a complex of organic and inorganic substances), covered the biofilm in the second half of its formation process producing a different community structure from that initially. This study revealed a fast and dynamic process of biofilm formation on the reed surface of reed.