Rice is one of the most important cereals, especially in Asian countries. Methane (CH₄), one of the major greenhouse gases, is emitted from flooded paddy fields as a result of phenomena on various scales. This paper review studies on CH₄ emission from paddy fields, paying special attention to mitigation options from the viewpoint of their feasibility on a field scale. Field management of rice paddies is primarily carried out to obtain suitable rice yields, but it also has physical, chemical, and biological effects on CH₄ emission. Therefore, some management practices can be win-win options that sustain rice yield and mitigate CH₄ emission. For example, appropriate water management for rice growth and yield is also effective in decreasing CH₄ emission. Other practices, such as nitrogen fertilizer application and organic matter application can also have positive effects on rice yield and CH₄ emission. Recent microbial studies have been revealing the ecology of methanogens and methanotrophs in paddy soils. Further studies on a microbial scale will offer additional clues to the mitigation of CH₄ emission from paddy fields.

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To study the resistance of biofilms to antibiotics, it is necessary to screen for mutant bacteria which are sensitive to antibiotics. To screen a vast number of mutants, we used a red pigment of Serratia marcescens strain 274 as a marker which could be identified by the naked eye. With this method, we selected ampicillin (ABPC)-sensitive biofilm-forming mutants from among S. marcescens transposon5 (Tn5) mutants. Four groups were screened and three were analyzed genetically. The Tn5 inserted gene of two groups was thought to be concerned with the formation of exopolysaccharides. The other group has an insertion of Tn5 into a gene which has high sequence similarity to the gene for ferric enterobactin-binding protein. It, however, was confirmed that all of the screened mutants formed ABPC-sensitive biofilms. Therefore this method was demonstrated to be beneficial for the screening of antibiotic-sensitive biofilm-forming mutants.

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We enriched a pentachlorobenzene (pentaCB)-dechlorinating microbial consortium from an estuarine-sediment sample obtained from the mouth of the Arakawa River. The sediment was incubated together with a mixture of four electron donors and pentaCB, and after five months of incubation, the microbial community structure was analyzed. Both DGGE and clone library analyses showed that the most expansive phylogenetic group within the consortium was affiliated with the phylum Chloroflexi, which includes Dehalococcoides-like bacteria. PCR using a degenerate primer set targeting conserved regions in reductive-dehalogenase-homologous (rdh) genes from Dehalococcoides species revealed that DNA fragments (approximately 1.5-1.7 kb) of rdh genes were amplified from genomic DNA of the consortium. The deduced amino acid sequences of the rdh genes shared several characteristics of reductive dehalogenases. The mixed culture could be maintained by transferring small inocula into fresh synthetic mineral medium containing either acetate or pyruvate, which supported the dechlorination of pentaCB by acting as an electron donor.

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In this study, we developed a comprehensive method for monitoring representative harmful algal bloom (HAB) species in Japan, namely, three dinoflagellates, Cochlodinium polykrikoides, Karenia mikimotoi, Heterocapsa circularisquama, and four raphidophycean flagellates, Chattonella antiqua, C. marina, C. ovata, and Heterosigma akashiwo; this was done by using a real-time PCR assay with primer sets and probes based on species-specific sequences in the D1/D2 region of 28S rRNA genes. For comprehensive monitoring, a DNA extraction protocol using cetyltrimethylammonium bromide (CTAB) was used. In this quantitative PCR assay, specially designed primer sets and probes showed species-specificity and even 1 cell of each harmful alga was detectable. Detection and quantification of HAB species were unaffected by either the growth phase of the algae or the existence of algae other than the target species in the culture. For environmental samples, this real-time PCR assay could be carried out more rapidly and easily, in addition to the similarity of the cell densities estimated by direct counting under a light microscope and by the real-time PCR assay. Moreover, the real-time PCR assay showed a higher sensitivity in seawater samples in which the harmful algae were not detected by direct counting.

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To clarify the genetic basis to the diversity of denitrifying ability in soybean bradyrhizobia, we compared the end-products of denitrification (N₂, N₂O and NO₂^-) with the existence of denitrifying genes (napA, nirK, norCB and nosZ) of sixty phylogenetically diverse strains of Bradyrhizobium japonicum and B. elkanii. The results indicate that the existence of denitrifying genes directly determines phenotype (end-products) in most strains of B. japonicum. The denitrifying capability and gene set were reflected by phylogenetic position based on repeated sequences (RS)-fingerprints and 16S rRNA gene sequences. However, the denitrifying genes in HRS (highly repeated sequence-possessing) strains of B. japonicum, which were identified based on RS-fingerprints as having heavy hybridization, resulted in an inconsistent correlation probably because of genomic rearrangements. The evolutionary and ecological implications of the denitrifying genes and capability in soybean bradyrhizobia are discussed.

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We surveyed the soils from 54 potato fields in Nagasaki during the 2003 and 2004 spring croppings, and examined the relationship between the detectable copy number of the nec1 gene at harvest and the incidence of scab disease in each field. The nec1 gene in soil samples was quantified by a quantitative competitive quenching probe PCR (QCQP-PCR) method, using primers specific to the nec1 gene and fluorescence quenching-based probes. A significant positive correlation (r²=0.8195) was observed between the detectable copy number of the nec1 gene and the incidence of disease in tubers from 21 fields in 2003. In 23 of 25 fields where the incidence of disease was >10%, more than 10³ copies of nec1 per g-soil were detected. Of the nine fields where the incidence of disease was <10%, eight had fewer than 10³ gene copies. The nec1 gene was not detected in 20 fields where no disease was found. These results suggest that scab disease occurs more frequently in fields where more than 10³ copies of nec1 per g-dry soil are detected.

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During the search for thermophilic myxobacteria in geothermal environments, four myxobacteria-like cultures that grew at temperatures of up to 50°C and optimally at 45-49°C were enriched from various hot springs in Japan. Three of the cultures were derived from freshwater hot springs and one from a coastal saline spring. Although all lacked fruiting structures, they were bacteriolytic and formed diffusive shallow crater-like colonies. Even after repeated enrichment procedures using Escherichia coli-prey agar media, the crater-like cultures were usually surrounded by thin, film-like, spreading colonies of other gliding bacteria that grew faster. Within the crater-like sunken area, rod-shaped bacterial cells were observed. 16S rRNA gene sequences from the myxobacterial cultures were amplified by nested PCR with myxobacteria-specific primers, subcloned, and phylogenetically analyzed. All of the myxobacterial clones obtained from the three cultures were assigned to the suborder Sorangineae. These clones were distantly positioned within this suborder, and mostly shown to represent new genera of myxobacteria. These results suggested that diverse species of moderately thermophilic myxobacteria, including many as yet undescribed, ubiquitously inhabit hot spring environments.

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