Escherichia coli is naturally present in the intestinal tracts of warm-blooded animals. Since E. coli is released into the environment through deposition of fecal material, this bacterium is widely used as an indicator of fecal contamination of waterways. Recently, research efforts have been directed towards the identification of potential sources of fecal contamination impacting waterways and beaches. This is often referred to as microbial source tracking. However, recent studies have reported that E. coli can become "naturalized" to soil, sand, sediments, and algae in tropical, subtropical, and temperate environments. This phenomenon raises issues concerning the continued use of this bacterium as an indicator of fecal contamination. In this review, we discuss the relationship between E. coli and fecal pollution and the use of this bacterium as an indicator of fecal contamination in freshwater systems. We also discuss recent studies showing that E. coli can become an active member of natural microbial communities in the environment, and how this bacterium is being used for microbial source tracking. We also discuss the impact of environmentally-"naturalized" E. coli populations on water quality.

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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. This minireview summarizes and discusses recent studies of endophytic bacteria residing in rice plants, focusing on flora, origin, movement, and interaction with plants/other microbes and referring to endophytes in other plants. The findings concerning bacterial flora obtained by cultural and non-cultural methods are also compared and discussed. Some attempts to apply endophytes to the rice plant and the resultant effects are introduced. The future perspective to deepen the study of endophytes in terms of both application and basic science is considered.

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Acetate is one of the most important intermediates for methanogenesis in the anaerobic mineralization of organic materials. Methanogenic acetate degradation is carried out by either an aceticlastic reaction or an anaerobic acetate-oxidizing reaction. In contrast to the former reaction, the latter is energetically extremely unfavorable. However, the oxidation of acetate can occur with syntrophic interaction between certain bacteria and methanogenic archaea. The bacteria, namely syntrophic acetate-oxidizing bacteria, can oxidize acetate to produce hydrogen/CO₂ only when their products are subsequently utilized by the hydrogen-scavenging methanogens. Surprisingly, some of these bacteria can also axenically grow on hydrogen/CO₂ to produce acetate. This means that the bacteria can utilize both substrates and products reversibly. This review describes current studies of these curious and fascinating microbes.

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The present study was conducted with the aim of finding a suitable delivery method for introducing endophytic bacteria into new sugarcane stalks. Stem pieces of cultivars NiF8 and Ni15 were inoculated with Herbaspirillum sp. strain B501gfp1 by the vacuum infiltration method. The inoculated bacteria showed higher levels of nitrogenase activity in cultivar Ni15 than NiF8. The population density immediately after inoculation (10⁷ CFU g [fresh weight]^-1) showed that strain B501gfp1 successfully entered the stem tissues of Ni15, where its presence was confirmed by fluorescence microscopic observations. Colonization was observed in the intercellular spaces and between the cell layers. The population of inoculated bacteria remained stable at 5 days after inoculation. The inoculated stems also showed adequately strong acetylene reduction activity compared to uninoculated stems in the absence of indigenous nitrogen-fixing bacteria.

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A trial was conducted to suppress bacterial wilt of tomato (BWT) caused by Ralstonia solanacearum using biocontrol agents (BCAs) isolated from soils in Kalimantan, Indonesia. Five isolates were selected from 270 isolates as better performing BCAs through screening four times using a pumice medium. The isolates selected were identified as Burkholderia nodosa, Burkholderia sacchari, Burkholderia pyrrocinia and Burkholderia terricola according to 16S rDNA sequences, fatty acid composition and carbon source utilization patterns. Among them, B. nodosa G5.2.rif1 had significant suppressive effects on Fusarium wilt of tomato (FWT) and spinach (FWS) as well as BWT. When B. nodosa G5.2rif1 was inoculated into a pumice medium in combination with sucrose, it showed even more stable disease suppression for BWT, but not for FWS. This suppression was considered to mainly occur through competition for nutrients. In two times greenhouse experiments for BWT using pots comparable in size to those used commercially, B. nodosa G5.2rif1 significantly suppressed the disease index by 33-79%, with no inhibitory effects on the growth, yield and quality of tomatoes.

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Changes in the bacterial community in soil-water suspensions during the enrichment period of 2,4-D and 2,4,5-T degraders were examined using denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rRNA gene. The nucleotide sequences of almost all major bands at the degradation of 2,4-D and 2,4,5-T corresponded to those of 2,4-D- and 2,4,5-T-degrading isolates, and successions of diverse 2,4-D- and 2,4,5-T-degrading bacterial communities were demonstrated in the DGGE profile. These results suggested that 2,4-D- and 2,4,5-T-degrading isolates were responsible for the degradation of 2,4-D and 2,4,5-T in soil-water suspensions; however, one major band of a non-degrader was found in some cases. Therefore, to elucidate the relationship between the structures and functions of bacterial communities, the importance of a combined approach using both culture-dependent and -independent methods was demonstrated.

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Spatial monitoring of tetracycline (TC)-resistant bacteria in sediments of the Mekong River watershed revealed that the main waterway showed a high occurrence rate of TC-resistant bacteria, whereas Tonle Sap Lake and the Sai Gon estuary did not. The Shannon index (H'), an indicator of ecological diversity, was calculated from denaturing gradient gel electrophoresis (DGGE) profiles, which indicated that the main waterway of the Mekong River had high microbial diversity (high H') compared to Tonle Sap Lake and the Sai Gon estuary; this diversity was positively correlated with the occurrence rate of TC-resistant bacteria. Analysis of ribosomal protection protein (RPP) genes tet(M), tet(S) and tet(W) in the same area also revealed that high diversity was positively correlated with the occurrence rate of RPP genes, suggesting that RPP genes are well conserved across various bacterial species. Further evidence of different genotypes of tet(M) suggests that the drug resistance genes likely have various origins, and are mixed in the sediment. Sediments in this area are therefore potential reservoirs of drug resistance genes.

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A total of eighty-one Escherichia coli isolates belongs to forty-three different serotypes including several pathogenic strains such as enterotoxigenic E. coli (ETEC), enterohaemorrhagic E. coli (EHEC), enteropathogenic E. coli (EPEC) and uropathogenic E. coli (UPEC) isolated from a tropical estuary were tested against 12 antibiotics to determine the prevalence of multiple antibiotic resistance (MAR), antimicrobial resistance profiles and also to find out high risk source of contamination by MAR indexing. The results revealed that more than 95% of the isolates were multiple antibiotic resistant (resistant to more than three antibiotics). Resistance to vancomycin, novobiocin, kanamycin, oxytetracycline, tetracycline, streptomycin was high (>80%), resistance to other antibiotics was relatively less. The MAR indexing of the isolates showed that all these strains were originated from high risk source of contamination. The incidence of multiple antibiotic resistant E. coli especially the pathogenic strains in natural water will pose a serious health risk to the human population and also act as a `manmade' reservoir of resistance genes for (potentially) pathogenic bacteria. The determination of antibiotic susceptibility/resistance patterns of isolated microbes is a part of the microbial monitoring process of the water which would be important for the meaningful interpretation of sanitary water quality data.

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A series of additives were evaluated for their effects on improving the yield and quality of DNA extracted from recalcitrant soils. Levels of possible DNA contaminants in these supplements were also assessed. Three of the additives (skim milk, casein, and RNA) were shown to be effective in improving the stable extraction of DNA from recalcitrant samples of Andosol. However, whereas skim milk appeared to be the most effective additive for this purpose, our data indicated that this commercially sourced product contained considerable amounts of contaminant DNA (30 to 40 μg/g skim milk). A ribosomal intergenic spacer analysis (RISA) revealed the consistent contamination of different batches of this product with DNA of several species of both eukaryotes (cattle and protists) and prokaryotes. In particular, thermophilic bacteria such as Geobacillus and Anoxybacillus were identified in the sequenced PCR amplicons from skim milk. The results of the RISA clearly also indicated that the impact of contaminated DNA on the analysis of a microbial community could be significant when skim milk is used for extracting DNA from a recalcitrant soil. In contrast, only a trace amount of contaminating DNA was evident in casein and none was detected in the RNA examined in the present study.

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A total of 15 Rhodococcus erythropolis strains were characterized as antibiotic producers and classified into three groups according to their antibiotic spectrum and growth compatibility (strains within a group did not inhibit each other's growth). Each of the antibiotic groups exhibited antibiotic activity against a taxonomically different breadth of bacteria: Group I exhibited antibiotic activity against a broad range of Gram-positives; Group II, mainly against the genus Rhodococcus and some other Gram-positives; and Group III, particularly against R. erythropolis. The antibiotic compounds of the strains belonging to Groups I and II were partially purified from liquid culture media. It was found that each group produces distinct antibiotics. In contrast to the diversity of antibiotic activity, the sequence of the 16S rRNA gene in the analyzed 1,440-nt region was found to be identical in all these 15 Rhodococcus strains. In addition to the antibiotic diversity in R. erythropolis strains, we elucidated the diversity in antibiotic-producing species of the genus Rhodococcus. Thus far, only a few antibiotic-producing strains have been reported in Rhodococcus; however, our results demonstrated that the genus comprises diverse antibiotic producers, and is a good source of new antibiotics.

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Vibrio harveyi cause mass mortalities of cultured marine fish. To address the ecology of V. harveyi in aquaculture, intensive monitoring is needed. We first optimized a quantitative real-time PCR method to determine V. harveyi abundance. The designed TaqMan probe and primers based on the 16S rRNA gene were specific at 68°C of annealing and extension. Furthermore, the method using a chelating resin method was able to enumerate 1.7×10² CFU/ml in breeding seawater at an abalone farm. This method represents a good tool for monitoring the ecology of V. harveyi in marine environments within 5 h.

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