A wide variety of haloorganic compounds undergo reductive dehalogenation by certain anaerobic microorganisms. Metabolic reductive dehalogenation is coupled with energy-conserving respiratory electron transport in which a halogenated compound is used as the terminal electron acceptor, the biological process called dehalorespiration or halorespiration. Dehalorespiring bacteria may play important roles in the geochemical cycle with organohalogens in nature and have great promise in their application to the bioremediation of haloorganic contaminants derived from anthropogenic sources. During the past decade, a number of dehalorespiring microorganisms, including a unique group of strictly dehalorespiring bacteria, "Dehalococcoides", have been isolated and characterized at phylogenetic, physiologic, and genetic levels. Also, new perspectives of dehalorespiring bacteria have emerged based on information about genomics and molecular microbial ecology. This review article focuses on up-to-date knowledge of the biodiversity of dehalorespiring bacteria and reductively dehalogenating microbial consortia with special emphasis on those capable of transforming polychlorinated biphenyls and dioxins.

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Land to be remediated, such as those affected by heavy metals or organic pollutants, can be remediated using biological approaches. These include, quarries and strip mines, or land impacted by oil pollution or other organic pollutants. Phytoremediation is usually a key component of bioremediation. However, without restoring soil organic matter, the soil biodiversity takes decades to recover. The soil organisms are a key component of soil function, and support plant growth. In addition, the soil microbiology is essential both for bioremediation and supporting phytoremediation. Using inexpensive sources of quality organic matter, it should be possible to accelerate recovery of ecosystem health and biodiversity. One potential source of untapped organic matter is municipal solid waste as a composted amendment. The organic matter amendment promotes soil structure and the creation of adequate habitat and substrate for the soil decomposition food web. Long-term chronosequence studies indicate that soil food webs tend to make a transition after about 20 years to a stable community structure. This approach could be used to gain carbon credits by restoring degraded or polluted soils.

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Any modification of the environment that leads to a physiological, genetic, or epigenetic adaptive response in microorganisms may be considered as a stress. Historically, forms of stresses affecting biological structures were classified either as non-thermal, such as osmotic, oxidative, or acid stress or as thermal stress, hot or cold. Currently, the classification in biology is as abiotic, including physical and chemical stress, or biotic. The aim of this mini-review is to show, through the example of microorganisms, that the response to stress can be considered, in biology, as a global phenomenon, which can be extended to anthropogenic pressure.

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Fungal communities were isolated from surface sterilized leaf segments of nine ethnopharmaceutically important medicinal herbs collected from the Bhadra River Project Area, the Malnad region, Southern India. A total of 2159 isolates belonging to 55 different fungal species were isolated from 3600 leaf segments collected during the wet and dry seasons. Chaetomium globosum (7.3%), Aureobasidium pullulans (6.1%), Cladosporium cladosporioides (3.9%), Curvularia lunata (1.9%), Nigrospora oryzae (1.7%), Alternaria alternata (1.3%), Botryosphaeria subglobosa (1.1%), Phoma multirostrata (0.9%), Aspergillus niger (0.8%), Fusarium oxysporum (0.7%), Rhizoctonia solani (0.4%), and Sphaeropsis sapenea (0.3%) were the most frequently isolated fungal species. Colonization rates of fungal species varied significantly between the two seasons. Host specificity was observed in some host plants.

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The influences of chemical fertilizers and a nitrification inhibitor on greenhouse gas fluxes (N₂O and CH₄) in a corn field in Indonesia were investigated using a closed chamber. Plots received 45+45 kg-N ha^-1 of nitrogen fertilizer by split applications of urea, a single application of controlled-release fertilizer (CRF-LP30) or urea+dicyandiamide (DCD; a nitrification inhibitor), and no nitrogen application (control). Cumulative amounts of N₂O emitted from the field were 1.87, 1.70, 1.06, and 0.42 kg N₂O-N ha^-1 season^-1 for the urea, CRF-LP30, urea+DCD, and control plots, respectively. The application of urea+DCD reduced the emission of N₂O by 55.8% compared with urea. On the other hand, the soil acted as a sink for CH₄ in the CRL-LP30, control, and urea+DCD plots with value of −0.09, −0.06 and −0.06 kg CH₄-C ha^-1 season^-1, respectively. When the viability of AOB (ammonia-oxidizing bacteria) and NOB (nitrite-oxidizing bacteria) were monitored, AOB numbers were correlated with the N₂O emission. These results suggest that 1) there is a potential for reducing emissions of N₂O by applying DCD, and 2) corn fields treated with CRF or urea+DCD can act as a sink for CH₄ in a tropical humid climate.

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We have developed a new system for the rapid diagnosis of soil-borne diseases, consisting of two biosensors. The system was constructed using equal quantities of two different microbes, each individually immobilized on an electrode. These two sensors were coupled as a dual sensor system and used for simultaneous measurements. Measurements were carried out by immersing the microbial sensors in a soil extract. When microbial respiration increased with the assimilation of organic compounds in the sample, the decrease of the dissolved oxygen concentration was measured with an oxygen electrode. Initially, three pathogen-infested soils were compared to two non-diseased soils using the system. The ratio of responses to both non-diseased soils was higher than that to infested soils. Subsequently, we used the biosensor system to investigate the effect of six antagonists on the inhibition of four diseases. The correlation between the development of symptoms and ratio to responses was estimated. The ratio between the responses of the two sensors correlated with symptoms, except for two samples where the antagonist promoted the disease's development.

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The cellular slime mold Dictyostelium discoideum grows as unicellular free-living amoebae in the presence of nutrients. Upon starvation, the amoebae aggregate and form multicellular structures that each consist of a stalk and spores. D. discoideum encodes at least four proteins (Sir2A, Sir2B, Sir2C, and Sir2D) homologous to human SIRT. RT-PCR and WISH analyses showed that the genes for Sir2A, Sir2C, and Sir2D were expressed at high levels in growing cells but at decreased levels in developing cells, whereas the gene encoding Sir2B was expressed in the prestalk-cell region in the developmental phase.

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To examine the effect of vegetation type and grassland management regimen on the distribution of humus-degrading microorganisms, populations of humic acid-degrading (HAD) bacteria and fungi at three Andosol sites were investigated using the dilution plate method. Each site had three different vegetation types (Eulalia grassland, bamboo grassland, and coniferous plantations). Among the six grassland sites, two were maintained by burning and the others by cutting. HAD microorganisms were found in all soil samples. Low densities and small percentages of HAD bacteria were detected with no significant differences in the number of bacteria found between different vegetation types and grasslands managed in different ways. In contrast, the densities and percentages of HAD fungi differed according to vegetation type and management regimen. Specifically, the percentages of HAD fungi were significantly higher for burned grasslands. At burned sites, the numbers and percentages of HAD bacteria remained at a consistently low level, and no distinct seasonal changes were observed. In contrast, marked seasonal fluctuations in HAD fungi were detected. The percentages of these fungi remained relatively high between April and December. These fluctuations are likely due to the effects of burning on soil microorganisms.

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The bacterial community structure in soil of a tropical rainforest in East Kalimantan, Indonesia, where forest fires occurred in 1997-1998, was analysed by denaturing gradient gel electrophoresis (DGGE) with soil samples collected from the area in 2001 and 2002. The study sites were composed of a control forest area without fire damage, a lightly-burned forest area, and a heavily-burned forest area. DGGE band patterns showed that there were many common bacterial taxa across the areas although the vegetation is not the same. In addition, it was indicated that a change of vegetation in burned areas brought the change in bacterial community structure during 2001-2002. It was also indicated that, depending on a perspective, community structure of soil bacteria in post-fire non-climax forest several years after fire can be more heterogeneous compared with that in unburned climax forest. The dominant soil bacteria in the field of the present study were Acidobacteria, Actinobaceria, and Alphaproteobacteria based on the DNA sequences of DGGE bands, although they were not dominant among the culturable bacteria from the same soil samples.

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Soil environmental variability and fungal community structures were analyzed to evaluate differences in soils managed under organic (ORG) and conventional (CNV) systems of farming in Fukushima and Yamagata prefectures in Japan. The soils were collected from 8 ORG and 13 CNV farms in 2005, and 6 ORG and 13 CNV farms in 2006. Principal component analysis (PCA) of 26 environmental variables demonstrated that plots of ORG and CNV were separated; however, the differences were unclear. Environmental variability and scores of principal components indicated more MgO, available phosphorous, NO₃-N, and K₂O in ORG than in CNV, and more silt, Mn, and Mg/K in CNV than in ORG. The differences were considered distinguishing for these farming systems. The fungal DGGE profiles and characteristic band intensities could not be used to distinguish between ORG and CNV. However, the PCA of band profiles slightly differentiated the plots of each system for both 2005 and 2006, as was the case for environmental variability. Furthermore, analysis of the PCA scores revealed several characteristic bands in DGGE profiles. A sequence analysis of the characteristic bands indicated the genus Mortierella sp. and close relatives of Cheatomium globosum to be characteristic fungi in CNV, although definitive characteristic fungi were not found in ORG. Since these results were obtained from soils differing in the type and amount of fertilizer, the application of pesticide, and management system, they are considered to reflect the general difference between ORG and CNV soils.

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The role of microbes in the early development of ecosystems on new volcanic materials seems to be crucial to primary plant succession but is not well characterized. Here we analyzed the bacterial community colonizing 22-year-old volcanic deposits of the Miyake-jima Island (Japan) using culture-based and 16S rRNA gene clone library methods. The majority of 91 bacterial isolates were placed phylogenetically in two clusters (A and B) of the Betaproteobacteria. Cluster A (82% of isolates) was related to the genus Limnobacter and Cluster B (9%) was affiliated with the Herbaspirillum clade. The clone library analysis supported the predominance of Cluster B rather than Cluster A. Strain KP1-50 of Cluster B was able to grow on a mineral medium under an atmosphere of H₂, O₂, and CO₂ (85:5:10), and characterized by its large-subunit gene of ribulose 1,5-bisphosphate carboxylase/oxygenase (rbcL) and nitrogenase reductase gene (nifH). In contrast, strains of Cluster A did not grow chemolithoautotrophically with H₂, O₂, and CO₂ but increased their cell biomass with the addition of thiosulfate to the succinate medium, suggesting the use of thiosulfate as an energy source. From phenotypic characterization, it was suggested that the Cluster A and B strains were novel species in the genus Limnobacter and Herbaspirillum, respectively.

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Endophytic clostridia present on various plants as obligate anaerobes were surveyed by terminal restriction fragment length polymorphism (TRFLP) analysis specific to the clostridial 16S rRNA gene. Endophytic clostridia were detected in 10 plant types: sugarcane, cultivated rice, corn, tobacco, soybean, bermuda grass, tall fescue, and three mangrove species. Phylogenetically, cluster XIVa clostridia were detected more frequently than cluster I clostridia in aerial parts. Isolation of clostridia from surface-sterilized sugarcane stem validated the TRFLP results. Plant-derived clostridia occupied two unique phylogenetic positions (groups I and II) within cluster XIVa. Most of cluster XIVa clostridia from other sources (e.g., human, animal, and insect intestines) were located outside these groups. Thus two unique groups of cluster XIVa clostridia are widely distributed in plants, including crops. In field-grown soybeans, TRFLP analysis revealed clostridia only in a non-nodulating mutant. Ribosomal intergenic spacer analysis (RISA) showed that the bacterial community in soybean shoot depended partly on the soybean nodulation genotype.

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Beard worms (Siboglinidae, Polychaeta), which lack a mouth and a digestive tract, harbor thioautotrophic or methanotrophic bacteria in special cells called bacteriocytes. These endosymbionts have been considered to be trapped at a specific larval stage from the environment. Although many species of beard worms have been discovered in various abyssal seas, Oligobrachia mashikoi inhabits Tsukumo Bay which is only 25 m deep. At least seven types of endosymbionts (endosymbiont A-G) have been distinguished in O. mashikoi. In this study, we investigated the distribution pattern of free-living cells related to the major endosymbiont (endosymbiont A) in Tsukumo Bay by quantitative PCR targeting the 16S rRNA gene. The endosymbiont A-related phylotype was detected in almost all sediment samples collected from 23 points in Tsukumo Bay, ranging in copy number of the 16S rRNA gene from 2.22×10⁴ to 1.42×10⁶ copies per gram of dry-sediment. Furthermore, the free-living cells made up less than 9% of the total eubacterial population, suggesting that the O. mashikoi larvae precisely select candidates for their endosymbiont from bacterial flora in the environment. This is the first report on the ecological characterization of a free-living bacterium related to the endosymbiont of the siboglinid polychaete, O. mashikoi.

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We examined the nitrogenase reductase (nifH) genes of endophytic diazotrophic bacteria expressed in field-grown sweet potatoes (Ipomoea batatas L.) by reverse transcription (RT)-PCR. Gene fragments corresponding to nifH were amplified from mRNA obtained from the stems and storage roots of field-grown sweet potatoes several months after planting. Sequence analysis revealed that these clones were homologous to the nifH sequences of Bradyrhizobium, Pelomonas, and Bacillus sp. in the DNA database. Investigation of the nifH genes amplified from the genomic DNA extracted from these sweet potatoes also showed high similarity to various α-proteobacteria including Bradyrhizobium, β-proteobacteria, and cyanobacteria. These results suggest that bradyrhizobia colonize and express nifH genes not only in the root nodules of leguminous plants but also in sweet potatoes as diazotrophic endophytes.

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Prokaryotic associations with gut protists of the termite Coptotermes formosanus were investigated based on 16S rRNA gene sequences. An endosymbiotic methanogen of Spirotrichonympha leidyi phylogenetically grouped with endosymbionts of other gut protists in the genus Methanobrevibacter, seemed to be unrelated to the host protist phylogeny. Three different lineages of ectosymbiotic spirochetes in the genus Treponema were identified in single cells of Holomastigotoides mirabile, indicating their simultaneous occurrence. Although these symbionts represented mere minor populations in the gut, their phylogenetic assignments suggest a common symbiotic relationship involving H₂ metabolism.

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