Root-nodule bacteria (rhizobia) are of great importance for nitrogen acquisition through symbiotic nitrogen fixation in a wide variety of leguminous plants. These bacteria differ from most other soil microorganisms by taking dual forms, i.e. a free-living form in soils and a symbiotic form inside of host legumes. Therefore, they should have a versatile strategy for survival, whether inhabiting soils or root nodules formed through rhizobia-legume interactions. Rhizobia generally contain large amounts of the biogenic amine homospermidine, an analog of spermidine which is an essential cellular component in most living systems. The external pH, salinity and a rapid change in osmolarity are thought to be significant environmental factors affecting the persistence of rhizobia. The present review describes the regulation of homospermidine biosynthesis in response to environmental stress and its possible functional role in rhizobia. Legume root nodules, an alternative habitat of rhizobia, usually contain a variety of biogenic amines besides homospermidine and the occurrence of some of these amines is closely associated with rhizobial infections. In the second half of this review, novel biogenic amines found in certain legume root nodules and the mechanism of their synthesis involving cooperation between the rhizobia and host legume cells are also described.

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Snow molds are a group of fungi that attack dormant plants under snow. In this paper, their survival strategies are illustrated with regard to adaptation to the unique environment under snow. Snow molds consist of diverse taxonomic groups and are divided into obligate and facultative fungi. Obligate snow molds exclusively prevail during winter with or without snow, whereas facultative snow molds can thrive even in the growing season of plants. Snow molds grow at low temperatures in habitats where antagonists are practically absent, and host plants deteriorate due to inhibited photosynthesis under snow. These features characterize snow molds as opportunistic parasites. The environment under snow represents a habitat where resources available are limited. There are two contrasting strategies for resource utilization, i.e., individualisms and collectivism. Freeze tolerance is also critical for them to survive freezing temperatures, and several mechanisms are illustrated. Finally, strategies to cope with annual fluctuations in snow cover are discussed in terms of predictability of the habitat.

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Seasonal changes in the abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) within the sand of an eelgrass (Zostera marina) zone were examined by a quantitative PCR of both crenarchaeotal and betaproteobacterial ammonia monooxygenase alpha subunit (amoA) genes together with temperature and concentrations of ammonium, nitrite, and nitrate from May 2007 to June 2008 at Tanoura Bay, Shizuoka, Japan. The abundance of both amoAs in the sand between May and June 2007 and between January and March 2008 was 1.5 to 2 orders of magnitude higher than the 10⁴ copies g^-1 of estimated amoA between September and December. Archaeal amoA was more diverse than betaproteobacterial amoA. Betaproteobacterial amoA clone libraries were dominated by Nitrosospira-like sequence types. An incubation experiment was conducted with sands collected in February 2008 and community structure was analyzed based on reverse-transcribed amoAs. RNA was extracted from sand incubated for 12 days at 30°C, 17 days at 20°C, and 80 days at 10°C. Different amoA clones were detected from in situ sand and incubated sand. This study reveals clear evidence of seasonal change in the abundance of AOA and AOB within the sand of an eelgrass zone.

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The splicing of a bacterial group II subclass B intron B.me.I1 from Bacillus megaterium chromosomes was investigated. RT-PCR and nucleic acid hybridization methods were used to understand the role of the intron-encoded protein (IEP) in the splicing of B.me.I1. An in vivo assay showed that the splicing occurred in the absence of IEP. An in vitro assay showed that B.me.I1 was spliced under conditions similar to those of the intracellular environment with no help from other biological molecules. Because all group II introns previously reported needed IEPs for their splicing in vivo, our results suggest that B.me.I1 is an "actual" self-splicing group II intron. This is also the first report to recognize the existence of group II introns that independently splice mRNA in vivo. The self-splicing of a bacterial intron may support that eukaryotic spliceosomal introns originated in bacterial genomes.

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A direct viable count procedure combined with fluorescence in situ hybridization (DVC-FISH) was developed for the specific detection and enumeration of viable Escherichia coli in cow manure. The DVC method was performed by trapping bacterial cells, extracted from cow manure samples, onto Nucleopore filters followed by incubation on a DVC medium containing yeast extract and four gyrase inhibitors. E. coli cells were identified by using the probe ES445. The DVC method efficiently promoted the elongation of E. coli cells and allowed for the recognition of individual cell division events, by observing microcolonies. Cell recovery by DVC-FISH together with bacterial extraction, was 53% with an inoculum of 10⁷ to 10¹⁰ cells g^-1 dry weight, when the manure samples were inoculated with a fresh culture of E. coli and determinations were made immediately. An examination of the survival of E. coli in a cow manure microcosm showed that an increasing fraction of E. coli became non-culturable but were still detectable by DVC-FISH. All these results suggest that DVC-FISH is useful for enumerating viable, even non-culturable, E. coli in cow manure.

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Plastic debris causes extensive damage to the marine environment, largely due to its ability to resist degradation. Attachment on plastic surfaces is a key initiation process for their degradation. The tendency of environmental marine bacteria to adhere to poly(ethylene terephthalate) (PET) plastic surfaces as a model material was investigated. It was found that the overall number of heterotrophic bacteria in a sample of sea water taken from St. Kilda Beach, Melbourne, Australia, was significantly reduced after six months from 4.2-4.7×10³ cfu mL^-1 to below detectable levels on both full-strength and oligotrophic marine agar plates. The extinction of oligotrophs after six months was detected in all samples. In contrast, the overall bacterial number recovered on full strength marine agar from the sample flasks with PET did not dramatically reduce. Heterotrophic bacteria recovered on full-strength marine agar plates six months after the commencement of the experiment were found to have suitable metabolic activity to survive in sea water while attaching to the PET plastic surface followed by the commencement of biofilm formation.

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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.

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The amount of trehalose in cells of the cyanobacterium Spirulina (Arthrospira) platensis increased rapidly when a high concentration of NaCl was added to the culture medium. Inhibition of sodium ion transport by amiloride and monensin significantly decreased the amount of cellular trehalose, suggesting that the influx of sodium ions into the cells is coupled with the accumulation of trehalose. The amount of maltooligosyl trehalose hydrolase (Mth) which produces trehalose from maltooligosyl trehalose increased gradually after the increase in cellular trehalose. The gene for Mth was cloned and identified by Southern blot analysis. Real time RT-PCR analysis revealed that the expression of mth was enhanced by the addition of NaCl to the culture medium. It was concluded that both catalytic activity of Mth and the synthesis of Mth protein were enhanced by the addition of NaCl to the cells.

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Microbial community dynamics with metabolically active bacteria during the start-up operation of a personal fed-batch composting (FBC) reactor were studied. The FBC reactor was loaded daily with household garbage for 2 months. Metabolically active bacteria were monitored by the redox-dye-staining method using 5-cyano-2,3-ditoryl tetrazolium chloride (CTC), and the fluorescent formazans thus produced were detected by epifluorescence microscopy and flow cytometry (FCM). Microscopic CTC-positive (CTC+) counts accounted for 75-84% of the direct total count during the first week of operation and 19-35% thereafter. Slightly higher CTC+ counts were obtained by FCM. Culture-independent approaches by quinone profiling and denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA genes showed that a drastic population change from ubiquinone-containing members of the Proteobacteria to the Actinobacteria took place during the overall period of operation. The PCR-DGGE analysis of FCM-sorted CTC+ cells supported this observation but gave different major clones from those detected in the total community in some cases. These results suggest that metabolically active bacteria as measured by CTC staining are not always predominant in the FBC process.

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We examined N₂O emissions from the rhizosphere of field-grown soybeans during the late growth stage (99-117 days after sowing). Marked emissions were detected from the nodulated root systems of field-grown soybeans, whereas a non-nodulating soybean mutant showed no emission. Degraded nodules exclusively generated the N₂O. A culture-independent analysis of microbial communities showed Bradyrhizobium sp., Acidvorax facilis, Salmonella enterica, Xanthomonas sp., Enterobacter cloacae, Pseudomonas putida, Fusarium sp., nematodes, and other protozoans to be more abundant in the degraded nodules, suggesting that some of these organisms participate in the N₂O emission process in the soybean rhizosphere.

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Effects of plant litter type (larch needle-leaves, mixed broad-leaves, and sasa green leaves) and nutrient addition (nitrogen and phosphorus) on bacterial community-level physiological profiles (CLPPs) of a forest soil were examined using BIOLOG EcoPlates^TM. Both the litter and nutrient additions significantly increased color development in most of the wells in the BIOLOG microplates, with the effect of the latter being especially great for soils amended with plant leaves low in nutrients. Nitrogen addition to soils decreased the color development of some nitrogenous substrates. Litter type had a dominant effect on the CLPPs. The addition of nitrogen also strongly affected the CLPPs.

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Clone libraries were used to evaluate the effects of 2,4-dinitroanisole (DNAN) and n-methyl-4-nitroaniline (MNA) on bacterial populations within three anaerobic bioreactors. Prior to the addition of DNAN and MNA greater than 69% of the clones in each reactor were identified as a single Desulfuromonales species. However, after 60 days of treatment the Desulfuromonales distribution decreased to less than 13% of the distribution and a clone identified as a Levilinea sp. became the dominant organism at greater than 27% of the clone distribution in each reactor suggesting the species may play an important roll in the reduction of DNAN and MNA.

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Volume 23, no. 4, page 341, 2008.
Fig. 3. A bar for sample 9 was absent. The correct version of this figure is shown below.

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