A body of data has been amassed in recent years, which shows the existence of introns within rRNA gene loci of certain archaeal lineages. Most striking is that the introns are optional, present in some strains and absent in others. They often have a nested gene encoding a LAGLIDADG-type site-specific DNA endonuclease known as "homing endonuclease (HE)". Such introns are, therefore, assumed to be "mobile introns", which propagate horizontally by using the "homing" pathway.
The phenomenon whereby mobile introns are inserted into the archaeal rRNA gene loci and disperse within a population to create genome polymorphism can be interpreted as "selfish behavior" of HE genes. The intron-encoded HE does not break rRNA genes containing the introns, but acts selectively to break only the intronless alleles. In other words, HE destroys alleles which do not possess internally a copy of its own gene by introducing a double strand DNA break (DSB), thus endangering the continued existence of the host's genome in that failure to repair the DSB will prove lethal. Moreover, in making its own gene into a mould for the purpose of recombination, it is adopting the horizontal propagation strategy to increase the copy number of its own gene within the population.
HE is a vital factor in the propagation of this type of mobile intron, and it is a noteworthy fact that the HE gene is "neutral", being neither advantageous nor disadvantageous to the existence of the host. Since the HE gene is removed along with the intron in the splicing process, it has no effect on the functional expression of the rRNA gene. Here, we discuss the dynamics whereby these molecular parasites, which reside in the archaeal genomes, propagate and evolve within a population.

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Two dodecyltrimethylammonium bromide (DTAB)-degrading bacteria were isolated from activated sludge of a wastewater treatment plant (WWTP). The bacteria identified as Pseudomonas fluorescens was called F2 and F7. The BOD biodegradability of DTAB by these bacteria were relatively high and similar to that of the activated sludge. F7 grew in a basal medium containing DTAB as the sole carbon source, producing trimethylamine (TMA) from DTAB by a N-dealkylation process. Then, the intermediate TMA was degraded to dimethylamine (DMA) by N-dimethylation as a second step. The pathway of the degradation of DTAB by this strain was the same as that of the activated sludge. On the other hand, Ps. fluorescens F2 degraded DTAB to TMA, but TMA was not further degraded. As for Ps. fluorescens F7 degrading activity, anionic compounds, such as fatty acids and sodium dodecyl sulfates (SDS), enhanced the degradation and dodecanoate became the carbon and energy source for this bacteria strain. These results demonstrate that monoalkyl quaternary ammonium compounds are ultimately degraded through N-dealkylation and mineralization, by a bacterium isolated from activated sludge.

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Field and greenhouse experiments were conducted to investigate the seasonal dynamics of microbial communities of iron(III)-reducing bacteria (IRB) in irrigated paddy soils as affected by rice cultivation system history, aerated fallow, and soil till practice at the International Rice Research Institute (IRRI). IRB were enumerated by a modified Most Probable Number (MPN) method. The average numbers of glucose-, acetate- and benzoate-utilizing iron(III)-reducing bacteria in the dry season of 1999 were 5.2×10 ⁸, 1.2×10⁶, and 5.3 ×10⁵ g^-1 dry soil respectively in the double cropping field and 5.4×10⁷, 5.9×10⁵ and 6.9×10 ⁵ g^-1 dry soil respectively in the triple cropping field. In the wet season of the same year, they were 1.5×10⁵, 8.3×10 ³ and 1.1×10⁵ g^-1 dry soil respectively in the double cropping field; and 6.4×10 ⁵, 7.0×10⁵ and 2.7 ×10⁵ g^-1 dry soil respectively in the triple cropping field. The MPN values of these IRB have different seasonal dynamics under the influence of rice cultivation history and fallow treatment in paddy soils. The results of screening and identification of enriched IRB by the BIOLOG method showed that 66% of the tested strains could be identified, among them, 58% are Pseudomonas spp., which appeared to be the predominant species of iron(III) reducers in these paddy fields.

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In a simple laboratory microcosm constituted of riverbed sediment and its associated water, rapid degradation of herbicide atrazine mainly to cyanuric acid occurred through microbial degradation. To elucidate the role and behavior of microbes involved in atrazine degradation, comparative microcosms constituted of different sediment/water conditions and constitutions were employed. Fluorescence microscopic observation and direct bacterial count by DAPI (4',6-diamidino-2-phenylindole)-staining and CFU (colony forming unit) count by the plate method were also conducted to supplement the comparative study. As a result, planktonic microbes in the aqueous phase appeared not to be responsible for the initial degradation of atrazine, at least during the present experimental period of 70 days. The sediment was found to be important as a source of degrading microbes. However, once the degradation was initiated, the degrading activity in the aqueous phase was maintained without the sediment. Although CFU in aqueous phase increased with time, this increase in cell number seemed not to reflect the degrading activity. Large, glittering and whole particles, supposed to be microbial cells, were observed by DAPI-staining in the aqueous phase under a microscopic field only when active atrazine-degradation occurred. Therefore, they might be involved in the degrading activity.

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Small subunit rDNA sequences of symbiotic archaea in the gut of two species of xylophagous cockroaches Panesthia angustipennis and Salganea taiwanensis were analyzed by PCR. Most PCR clones obtained from the cockroaches belonged to the order Methanosarcinales (XSAT4A cluster) and formed a cluster with Methanomicrococcus blatticola and PCR clones obtained from higher termites. Affiliations of the symbiotic archaeal PCR clones of the XSAT4A cluster were closely related to those in the gut of higher termites. The results suggest that the archaeal community members of the XSAT4 cluster are widely distributed in xylophagous insects.

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We developed a new most-probable-number (MPN) method for enumeration of methanotrophs, using 48-well microtiter plates. With this method, a microtiter plate which has been inoculated with serial dilutions of a sample is placed in a plastic desiccator containing methane and shaken. The proposed method gave estimates of population densities of a pure culture of Methylocystis sp. strain M and of methanotrophs in a paddy soil sample similar to those obtained by a conventional MPN method using serum bottles. The new microtiter plate MPN method with an additional replica-plating technique made it possible to enumerate small populations of methanotrophs in cornfield and forest soils. It also requires less equipment, labor, and time than the conventional serum bottle MPN method.

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Recent reports have suggested the usefulness of a metabolic uncoupler to reduce excess sludge production in the activated sludge process. This study was conducted to more thoroughly study the effects of different chemical uncouplers on microbial biomass production, metabolic activity, and community structure in a laboratory-scale activated sludge system fed with synthetic sewage. Results showed that the amount of biomass produced decreased sharply with increasing concentrations of uncouplers in all cases. Among the five congeners of chlorophenols and nitrophenols as uncouplers studied, 4-nitrophenol was the most effective in reducing biomass production. The addition of 200 μM 4-nitrophenol resulted in a reduction in the biomass yield to less than 10% compared the control culture without the additive, while the BOD removal efficiency with the uncoupler remained approximately 80% of the control level. Differences in biomass reduction efficiency among the uncouplers tested suggested that uncouplers with a lower pK_a value have a higher potential to reduce biomass production. A short-term sequencing batch cultivation of sludge with any uncoupler exerted no or little effect on respiratory enzyme activities and the microbial community structure of the sludge. When the inhibitory effect of 4-nitrophenol on biomass production was studied in prolonged sequencing batch cultures, it was found to gradually diminish with time and had almost vanished after 4 weeks of operation. At this stage, a significant change in microbial community structure was demonstrated by respiratory quinone profiling. These results indicate that dosing an uncoupler in a short period is useful for minimizing excess sludge production in the activated sludge process without a significant decrease in BOD removal efficiency, but this positive effect is questionable over a long period of operation.

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Two promising bacterial strains, one isolated from the sediment surface of the study site (9410-O, mesophilic) and the other isolated from the Antarctic (AN-1, psychrotolerant) were used to enhance inorganic nitrogen (DIN) and phosphorus (DIP) regeneration in surface and bottom waters from a eutrophic coastal inlet in different seasons. Unfiltered waters with or without added bacteria were incubated in the dark at in situ water temperatures and at 10°C for 10-15 days, and the accumulation of DIN and DIP was monitored. Bacteria were always added as resuspensions prepared in filtered (0.2 μm) in situ waters. Strain 9410-O stimulated DIN and DIP net regeneration by ca. 2-6-fold in surface water, and 3-25-fold in bottom water at relatively high in situ/incubation temperatures viz. 23 and 26°C. However, it caused little enhancement of nutrient regeneration at 10°C. On the other hand, strain AN-1 stimulated net DIN and DIP regeneration in waters at both relatively high (23.5°C; 2-4-fold) and low temperatures (10-12°C; ca. 2-10-fold). Live cells of either strain yielded remarkably higher DIN releases than the same volume of killed counterparts indicating that the activities of the added bacteria rather than their utilization as organic matter were primarily responsible for additional nutrient regeneration.

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