Life-cycle analysis of environmental loads from household septic systems in Japan focusing on effluent water discharge.

Various types of small-scale wastewater treatment systems are widely used in rural areas, and life-cycle assessment (LCA) should be performed to evaluate their environmental performance. In this study, septic systems were first classified into five categories based on their wastewater treatment performance. Effluent samples from actual systems were collected, and their water qualities were determined. A model to evaluate the environmental load from the septic systems using LCA methods was then established. The water-quality values obtained were input to the model, and the life-cycle environmental costs of the classified septic systems were calculated. The mean environmental load of the effluent during the operation stage was 37.6%, confirming that evaluation of an effluent discharge inventory using LCA, inspection, and water-quality monitoring to improve operations is critical for reducing the environmental load. The operation stage accounts for over 99% of the involved eutrophication, biological toxicity, and toxic chemicals, which are strongly related to the quality of the effluent. Evaluation of the effluent discharge inventory using LCA is of great significance, even for small-scale wastewater treatment systems. The set of procedures developed in this study can be used to calculate comprehensive environmental impacts at wastewater treatment plants.

Type-specific quantification of particulate methane monooxygenase gene of methane-oxidizing bacteria at the oxic-anoxic interface of a surface paddy soil by digital PCR.

Aerobic methane-oxidizing bacteria (MOB) play an important role in mitigating methane emissions from paddy fields. In this study, we developed a differential quantification method for the copy number of pmoA genes of type Ia, Ib, and IIa MOB in paddy field soil using chip-based digital PCR. Three probes specific to the pmoA of type Ia, Ib, and IIa MOB worked well in digital PCR quantification when genomic DNA of MOB isolates and PCR-amplified DNA fragments of pmoA were examined as templates. When pmoA genes in the surface soil layer of a flooded paddy were quantified by digital PCR, the copy numbers of type Ia, Ib, and IIa MOB were 105 -106 , 105 -106 , and 107 copies g-1 dry soil, respectively, with the highest values in the top 0-2-mm soil layer. Especially, the copy numbers of type Ia and Ib MOB increased by 240% and 380% at the top layer after soil flooding, suggesting that the soil circumstances at the oxic-anoxic interfaces were more preferential for growth of type I MOB than type II MOB. Thus, type I MOB likely play an important role in the methane consumption at the surface paddy soil.

Evaluation of Disease Suppressiveness of Soils in Croplands by Co-Cultivation of Pathogenic Fusarium oxysporum and Indigenous Soil Microorganisms.

An evaluation of suppressiveness against soil-borne diseases is important for their control. We herein assessed disease suppression against F. oxysporum f. sp. spinaciae using the Fusarium co-cultivation method in 75 soils collected from croplands around the country. The suppressive effects of soil microbes against F. oxysporum growth were examined by simultaneously culturing soil suspensions and F. oxysporum f. sp. spinaciae on a culture medium. The growth degree of F. oxysporum on the medium varied among the 75 soils tested, and 14 soils showing different degrees of growth were selected to investigate the incidence of spinach wilt by cultivating spinach inoculated with the pathogenic F. oxysporum strain. A correlation (r=0.831, P<0.001) was observed between the disease incidence of spinach wilt and the growth degree of F. oxysporum using the co-cultivation method in the 14 selected soils. No correlations were noted between chemical and biological parameters (including pH and the population density of microbes, except for the growth degree of F. oxysporum) and the growth degree of F. oxysporum and incidence of spinach wilt, indicating that it was not possible to predict the degree of growth or disease incidence based on specific chemical and biological characteristics or their combination. The present results suggest that an evaluation of the growth degree of F. oxysporum by the Fusarium co-cultivation will be useful for diagnosing the disease suppressiveness of soil against pathogenic F. oxysporum in croplands.

Complete Genome Sequence of Ferrigenium kumadai An22, a Microaerophilic Iron-Oxidizing Bacterium Isolated from a Paddy Field Soil.

Ferrigenium kumadai An22T (= JCM 30584T = NBRC 112974T = ATCC TSD-51T) is a microaerophilic iron oxidizer isolated from paddy field soil and belongs to the family Gallionellaceae. Here, we report the complete genome sequence of F. kumadai An22T, which was obtained from the hybrid data of Oxford Nanopore long-read and Illumina short-read sequencing.

Dispersal history of Miniopterus fuliginosus bats and their associated viruses in east Asia.

In this study, we examined the role of the eastern bent-winged bat (Miniopterus fuliginosus) in the dispersion of bat adenovirus and bat alphacoronavirus in east Asia, considering their gene flows and divergence times (based on deep-sequencing data), using bat fecal guano samples. Bats in China moved to Jeju Island and/or Taiwan in the last 20,000 years via the Korean Peninsula and/or Japan. The phylogenies of host mitochondrial D-loop DNA was not significantly congruent with those of bat adenovirus (m2XY = 0.07, p = 0.08), and bat alphacoronavirus (m2XY = 0.48, p = 0.20). We estimate that the first divergence time of bats carrying bat adenovirus in five caves studied (designated as K1, K2, JJ, N2, and F3) occurred approximately 3.17 million years ago. In contrast, the first divergence time of bat adenovirus among bats in the 5 caves was estimated to be approximately 224.32 years ago. The first divergence time of bats in caves CH, JJ, WY, N2, F1, F2, and F3 harboring bat alphacoronavirus was estimated to be 1.59 million years ago. The first divergence time of bat alphacoronavirus among the 7 caves was estimated to be approximately 2,596.92 years ago. The origin of bat adenovirus remains unclear, whereas our findings suggest that bat alphacoronavirus originated in Japan. Surprisingly, bat adenovirus and bat alphacoronavirus appeared to diverge substantially over the last 100 years, even though our gene-flow data indicate that the eastern bent-winged bat serves as an important natural reservoir of both viruses.

Invention of Artificial Rice Field Soil: A Tool to Study the Effect of Soil Components on the Activity and Community of Microorganisms Involved in Anaerobic Organic Matter Decomposition.

Soils are characterized by diverse biotic and abiotic constituents, and this complexity hinders studies on the effects of individual soil components on microorganisms in soil. Although artificial soils have been used to overcome this issue, anoxic soils have not yet been examined. We herein aimed to create artificial soil that reproduces anaerobic methane production by soil from a rice field. Organic materials and mineral particles separated from rice field soil were mixed to prepare an artificial soil matrix; the matrix was added with a small volume of a soil suspension as a microbial inoculum. When the microbial inoculum was added immediately after matrix preparation, anaerobic decomposition was markedly less than that by original soil. When the inoculum was added 9-15 days after soil matrix preparation, anaerobic CO2 and methane production was markedly activated, similar to that by original soil after 40 days of incubation, which suggested that the maturation of the soil matrix was crucial for the reproduction of anaerobic microbial activities. The diversity of the microbial community that developed in artificial soil was markedly less than that in original soil, whereas their predicted functional profiles were similar. Humic substances altered the composition and network patterns of the microbial community. These results suggested that the functional redundancy of soil microorganisms was sustained by different microbial sub-communities. The present study demonstrated that artificial soil is a useful tool for investigating the effects of soil components on microorganisms in anoxic soil.

Quantification of hydrogen production by intestinal bacteria that are specifically dysregulated in Parkinson's disease.

Oral administration of hydrogen water ameliorates Parkinson's disease (PD) in rats, mice, and humans. We previously reported that the number of putative hydrogen-producing bacteria in intestinal microbiota is low in PD compared to controls. We also reported that the amount of hydrogen produced by ingestion of lactulose is low in PD patients. The decreased hydrogen production by intestinal microbiota may be associated with the development and progression of PD. We measured the amount of hydrogen production using gas chromatography by seven bacterial strains, which represented seven major intestinal bacterial groups/genera/species. Blautia coccoides and Clostridium leptum produced the largest amount of hydrogen. Escherichia coli and Bacteroides fragilis constituted the second group that produced hydrogen 34- to 93-fold lower than B. coccoides. Bifidobacterium pseudocatenulatum and Atopobium parvulum constituted the third group that produced hydrogen 559- to 2164-fold lower than B. coccoides. Lactobacillus casei produced no detectable hydrogen. Assuming that taxonomically neighboring strains have similar hydrogen production, we simulated hydrogen production using intestinal microbiota that we previously reported, and found that PD patients produce a 2.2-fold lower amount of intestinal hydrogen compared to controls. The lower amount of intestinal hydrogen production in PD was also simulated in cohorts of two other countries. The number of hydrogen-producing intestinal bacteria may be associated with the development and progression of PD. Further studies are required to prove its beneficial effect.

Ferrigenium kumadai gen. nov., sp. nov., a microaerophilic iron-oxidizing bacterium isolated from a paddy field soil.

An iron-oxidizing bacterium, designated strain An22T, which was isolated from a paddy field soil in Anjo, Japan, was described taxonomically. Strain An22T was motile by a single polar flagellum, curved-rod, Gram-negative bacterium that was able to grow at 12-37 °C (optimally at 25-30 °C) and at pH 5.2-6.8 (pH 5.9-6.1). The strain grew microaerobically and autotrophically by oxidizing ferrous iron, but did not form stalks, a unique structure of iron oxides. The major cellular fatty acids were C16 : 0 and C16 : 1ω7c/C16 : 1ω6c. The major respiratory quinones were UQ-10 and UQ-8. The strain possessed ribulose-1,5-bisphosphate carboxylase/oxygenase indicating an autotrophic nature via the Calvin-Benson-Bassham cycle. The total DNA G+C content was 61.4 mol%. 16S rRNA gene sequence analysis revealed that strain An22T was affiliated with the class Betaproteobacteria and clustered with iron-oxidizing bacteria, Gallionella ferrugineaJohan (94.8 % similarity) and Ferriphaselus amnicola OYT1T (94.4 %) in the family Gallionellaceae. Based on the low 16S rRNA gene sequence similarity to the phylogenetically closest genera and the combination of unique morphological, physiological and biochemical characteristics, strain An22T represents a novel genus and species within the family Gallionellaceae, for which the name Ferrigenium kumadai gen. nov., sp. nov. is proposed. The type strain is An22T (=JCM 30584T=NBRC 112974T=ATCC TSD-51T).

Evaluation of Suppressiveness of Soils Exhibiting Soil-Borne Disease Suppression after Long-Term Application of Organic Amendments by the Co-cultivation Method of Pathogenic Fusarium oxysporum and Indigenous Soil Microorganisms.

Preventive measures against soil-borne diseases need to be implemented before cultivation because very few countermeasures are available after the development of diseases. Some soils suppress soil-borne diseases despite the presence of a high population density of pathogens. If the suppressiveness of soil against soil-borne diseases may be predicted and diagnosed for crop fields, it may be possible to reduce the labor and cost associated with excessive disinfection practices. We herein evaluated the suppressiveness of soils in fields with the long-term application of organic amendments by examining the growth of pathogenic Fusarium oxysporum co-cultivated with indigenous soil microorganisms on agar plates. Soils treated with coffee residue compost or rapeseed meal showed suppressiveness against spinach wilt disease by F. oxysporum f. sp. spinaciae or spinach wilt and lettuce root rot diseases by F. oxysporum f. sp. spinaciae and F. oxysporum f. sp. lactucae, respectively, and the growth of pathogenic Fusarium spp. on agar plates was suppressed when co-cultured with microorganisms in a suspension from these soils before crop cultivation. These results indicate the potential of the growth degree of pathogenic F. oxysporum estimated by this method as a diagnostic indicator of the suppressiveness of soil associated with the inhabiting microorganisms. A correlation was found between the incidence of spinach wilt disease in spinach and the growth degree of F. oxysporum f. sp. spinaciae by this co-cultivation method, indicating that suppressiveness induced by organic amendment applications against F. oxysporum f. sp. spinaciae is evaluable by this method. The co-cultivation method may be useful for predicting and diagnosing suppressiveness against soil-borne diseases.

Transcription of mcrA Gene Decreases Upon Prolonged Non-flooding Period in a Methanogenic Archaeal Community of a Paddy-Upland Rotational Field Soil.

Methanogenic archaea survive under aerated soil conditions in paddy fields, and their community is stable under these conditions. Changes in the abundance and composition of an active community of methanogenic archaea were assessed by analyzing mcrA gene (encoding α subunit of methyl-coenzyme M reductase) and transcripts during a prolonged drained period in a paddy-upland rotational field. Paddy rice (Oryza sativa L.) was planted in the flooded field and rotated with soybean (Glycine max [L.] Merr.) under upland soil conditions. Soil samples were collected from the rotational plot in the first year, with paddy rice, and in the two successive years, with soybean, at six time points, before seeding, during cultivation, and after harvest as well as from a consecutive paddy (control) plot. By the time that soybean was grown in the second year, the methanogenic archaeal community in the rotational plot maintained high mcrA transcript levels, comparable with those of the control plot community, but the levels drastically decreased by over three orders of magnitude after 2 years of upland conversion. The composition of active methanogenic archaeal communities that survived upland conversion in the rotational plot was similar to that of the active community in the control plot. These results revealed that mcrA gene transcription of methanogenic archaeal community in the rotational field was affected by a prolonged non-flooding period, longer than 1 year, indicating that unknown mechanisms maintain the stability of methanogenic archaeal community in paddy fields last up to 1 year after the onset of drainage.

An Evaluation Method for Suppression of Pathogenic Fusarium oxysporum by Soil Microorganisms Using the Dilution Plate Technique.

Volume 31, No. 3, Page 307-313, 2016Page 310, Legend for Fig. 4 IncorrectFig. 4. Growth degree of Fusarium oxysporum f. sp. spinaciae for organic fertilizers at each dilution based on an estimation of the ellipse area (A) and extension length (B) of the colony. Cont, compound inorganic fertilizer; SBM, steamed bone meal; CDC, cow dung compost; MI, microbial inoculant. Values show mean of medians of degrees with SE (n=3). The ellipse area and extension length for control plates were 4,475 mm2 and 36.5 mm, respectively. CorrectFig. 4. Growth degree of Fusarium oxysporum f. sp. spinaciae for organic fertilizers at each dilution based on an estimation of the ellipse area (A) and extension length (B) of the colony. Cont, compound inorganic fertilizer; SBM, steamed bone meal; CDC, cow dung compost; MI, microbial inoculant. Values show mean of growth degrees with SE (n=3). The ellipse area and extension length for control plates were 4,475 mm2 and 36.5 mm, respectively. Page 311, Legend for Fig. 5 IncorrectFig. 5. Growth degree of Fusarium oxysporum f. sp. spinaciae for soil applied with organic fertilizers at each dilution based on an estimation of the ellipse area (A) and extension length (B) of the colony. Cont, compound inorganic fertilizer; SBM, steamed bone meal; CDC, cow dung compost; MI, microbial inoculant. Values show the mean of medians of degrees with SE (n=3). The ellipse area and extension length for control plates were 5,473 mm2 and 40.5 mm, respectively. CorrectFig. 5. Growth degree of Fusarium oxysporum f. sp. spinaciae for soil applied with organic fertilizers at each dilution based on an estimation of the ellipse area (A) and extension length (B) of the colony. Cont, compound inorganic fertilizer; SBM, steamed bone meal; CDC, cow dung compost; MI, microbial inoculant. Values show the mean of growth degrees with SE (n=3). The ellipse area and extension length for control plates were 5,473 mm2 and 40.5 mm, respectively. Page 312, Legend for Fig. 7 IncorrectFig. 7. Growth degree of Fusarium oxysporum f. sp. spinaciae at each dilution based on an estimation of the ellipse area (A) and extension length (B) of the colony. Cont, compound inorganic fertilizer; SBM, steamed bone meal; CDC, cow dung compost; MI2, microbial inoculant applied with 2,000 kg ha-1; MI10, microbial inoculant applied with 10,000 kg ha-1. Values show the mean of medians of degrees with SE (n=3). The ellipse area and extension length for control plates were 3,404 mm2 and 29.7 mm, respectively. CorrectFig. 7. Growth degree of Fusarium oxysporum f. sp. spinaciae at each dilution based on an estimation of the ellipse area (A) and extension length (B) of the colony. Cont, compound inorganic fertilizer; SBM, steamed bone meal; CDC, cow dung compost; MI2, microbial inoculant applied with 2,000 kg ha-1; MI10, microbial inoculant applied with 10,000 kg ha-1. Values show the mean of growth degrees with SE (n=3). The ellipse area and extension length for control plates were 3,404 mm2 and 29.7 mm, respectively. The authors would like to apologize for these corrections and any inconvenience caused.

Transcription of [FeFe]-Hydrogenase Genes during H2 Production in Clostridium and Desulfovibrio spp. Isolated from a Paddy Field Soil.

Changes in the relative abundances of the transcripts of hydA gene paralogs for [FeFe]-hydrogenase in Clostridium sp. strain H2 and Desulfovibrio sp. strain A1 isolated from paddy field soil were analyzed during H2 production. Strains H2 and A1 had at least five and two phylogenetically different hydA genes, respectively. The relative abundances of their hydA transcripts differed among the paralogs and H2 production activity changed in a manner that depended on the growth phase and conditions. Increases or decreases in the relative abundances of the transcripts of two out of five hydA genes in strain H2 correlated with changes in H2 production rates, whereas those of the others remained unchanged or decreased. In strain A1, the relative abundances of the transcripts of two hydA genes differed between monoculture, sulfate-reducing, and syntrophic, methanogenic conditions. The relative abundance of the transcripts of one hydA gene, predicted to encode a cytosolic [FeFe]-hydrogenase, was higher under syntrophic, methanogenic conditions than sulfate-reducing conditions, while that of the transcripts of the other hydA gene decreased with time under both conditions. This study showed that the transcription of the hydA gene during growth with active H2 production was differently regulated among the paralogs in H2 producers isolated from paddy field soil.

Effect of Elevated CO2 Concentration, Elevated Temperature and No Nitrogen Fertilization on Methanogenic Archaeal and Methane-Oxidizing Bacterial Community Structures in Paddy Soil.

Elevated concentrations of atmospheric CO2 ([CO2]) enhance the production and emission of methane in paddy fields. In the present study, the effects of elevated [CO2], elevated temperature (ET), and no nitrogen fertilization (LN) on methanogenic archaeal and methane-oxidizing bacterial community structures in a free-air CO2 enrichment (FACE) experimental paddy field were investigated by PCR-DGGE and real-time quantitative PCR. Soil samples were collected from the upper and lower soil layers at the rice panicle initiation (PI) and mid-ripening (MR) stages. The composition of the methanogenic archaeal community in the upper and lower soil layers was not markedly affected by the elevated [CO2], ET, or LN condition. The abundance of the methanogenic archaeal community in the upper and lower soil layers was also not affected by elevated [CO2] or ET, but was significantly increased at the rice PI stage and significantly decreased by LN in the lower soil layer. In contrast, the composition of the methane-oxidizing bacterial community was affected by rice-growing stages in the upper soil layer. The abundance of methane-oxidizing bacteria was significantly decreased by elevated [CO2] and LN in both soil layers at the rice MR stage and by ET in the upper soil layer. The ratio of mcrA/pmoA genes correlated with methane emission from ambient and FACE paddy plots at the PI stage. These results indicate that the decrease observed in the abundance of methane-oxidizing bacteria was related to increased methane emission from the paddy field under the elevated [CO2], ET, and LN conditions.

An Evaluation Method for the Suppression of Pathogenic Fusarium oxysporum by Soil Microorganisms Using the Dilution Plate Technique.

Soil-borne diseases caused by pathogenic microorganisms are one of the main factors responsible for the decline in crop yields in farmlands. Pathogenic Fusarium oxysporum causes serious damage to various crops, and, thus, a feasible diagnostic method for soil-borne diseases is required. We herein examined a simple method to evaluate the suppressiveness of soil microorganisms against a pathogen by co-cultivating indigenous soil microorganisms and a pathogenic fungus (F. oxysporum f. sp. spinaciae). We inoculated F. oxysporum onto the center of agar medium plates mixed with a dilution series of a suspension of organic fertilizers or soil. After an approximately one-week cultivation, the growth degree of F. oxysporum was estimated based on the size of the colonies that formed on the plates. The growth degree of F. oxysporum significantly differed among the organic fertilizers tested, indicating the usefulness of the method for evaluating suppressiveness by organic fertilizers. Differences in the growth degrees of F. oxysporum were associated with the incidence of disease in spinach on soil treated with organic fertilizers and inoculated with a pathogenic F. oxysporum strain. These results suggested that this method provides some useful information on the suppressiveness of organic fertilizers and soil against Fusarium wilt.

H2-Producing Bacterial Community during Rice Straw Decomposition in Paddy Field Soil: Estimation by an Analysis of [FeFe]-Hydrogenase Gene Transcripts.

The transcription patterns of [FeFe]-hydrogenase genes (hydA), which encode the enzymes responsible for H2 production, were investigated during rice straw decomposition in paddy soil using molecular biological techniques. Paddy soil amended with and without rice straw was incubated under anoxic conditions. RNA was extracted from the soil, and three clone libraries of hydA were constructed using RNAs obtained from samples in the initial phase of rice straw decomposition (day 1 with rice straw), methanogenic phase of rice straw decomposition (day 14 with rice straw), and under a non-amended condition (day 14 without rice straw). hydA genes related to Proteobacteria, Firmicutes, Bacteroidetes, Chloroflexi, and Thermotogae were mainly transcribed in paddy soil samples; however, their proportions markedly differed among the libraries. Deltaproteobacteria-related hydA genes were predominantly transcribed on day 1 with rice straw, while various types of hydA genes related to several phyla were transcribed on day 14 with rice straw. Although the diversity of transcribed hydA was significantly higher in the library on day 14 with rice straw than the other two libraries, the composition of hydA transcripts in the library was similar to that in the library on day 14 without rice straw. These results indicate that the composition of active H2 producers and/or H2 metabolic patterns dynamically change during rice straw decomposition in paddy soil.

Global change pressures on soils from land use and management.

Soils are subject to varying degrees of direct or indirect human disturbance, constituting a major global change driver. Factoring out natural from direct and indirect human influence is not always straightforward, but some human activities have clear impacts. These include land-use change, land management and land degradation (erosion, compaction, sealing and salinization). The intensity of land use also exerts a great impact on soils, and soils are also subject to indirect impacts arising from human activity, such as acid deposition (sulphur and nitrogen) and heavy metal pollution. In this critical review, we report the state-of-the-art understanding of these global change pressures on soils, identify knowledge gaps and research challenges and highlight actions and policies to minimize adverse environmental impacts arising from these global change drivers. Soils are central to considerations of what constitutes sustainable intensification. Therefore, ensuring that vulnerable and high environmental value soils are considered when protecting important habitats and ecosystems, will help to reduce the pressure on land from global change drivers. To ensure that soils are protected as part of wider environmental efforts, a global soil resilience programme should be considered, to monitor, recover or sustain soil fertility and function, and to enhance the ecosystem services provided by soils. Soils cannot, and should not, be considered in isolation of the ecosystems that they underpin and vice versa. The role of soils in supporting ecosystems and natural capital needs greater recognition. The lasting legacy of the International Year of Soils in 2015 should be to put soils at the centre of policy supporting environmental protection and sustainable development.

Methylomagnum ishizawai gen. nov., sp. nov., a mesophilic type I methanotroph isolated from rice rhizosphere.

An aerobic, methane-oxidizing bacterium (strain RS11D-PrT) was isolated from rice rhizosphere. Cells of strain RS11D-PrT were Gram-stain-negative, motile rods with a single polar flagellum and contained an intracytoplasmic membrane system typical of type I methanotrophs. The strain utilized methane and methanol as sole carbon and energy sources. It could grow at 20­37 °C (optimum 31­33 °C), at pH 6.8­7.4 (range 5.5­9.0) and with 0­0.2 % (w/v) NaCl (there was no growth at above 0.5 % NaCl). pmoA and mmoX genes were present. The ribulose monophosphate and/or ribulose bisphosphate pathways were used for carbon assimilation. Results of sequence analysis of 16S rRNA genes showed that strain RS11D-PrT is related closely to the genera Methylococcus, Methylocaldum, Methyloparacoccus and Methylogaea in the family Methylococcaceae. The similarity was low (94.6 %) between strain RS11D-PrT and the most closely related type strain (Methyloparacoccus murrellii R-49797T). The DNA G+C content was 64.1 mol%. Results of phylogenetic analysis of the pmoA gene and chemotaxonomic data regarding the major cellular fatty acids (C16 : 1ω7c, C16 : 0 and C14 : 0) and the major respiratory quinone (MQ-8) also indicated the affiliation of strain RS11D-PrT to the Methylococcus­Methylocaldum­Methyloparacoccus­Methylogaea clade. On the basis of phenotypic, genotypic and phylogenetic characteristics, strain RS11D-PrT is considered to represent a novel genus and species within the family Methylococcaceae, for which the name Methylomagnum ishizawai gen. nov., sp. nov. is proposed. The type strain is RS11D-PrT ( = JCM 18894T = NBRC 109438T = DSM 29768T = KCTC 4681T).

Elevated atmospheric CO2 levels affect community structure of rice root-associated bacteria.

A number of studies have shown that elevated atmospheric CO2 ([CO2]) affects rice yields and grain quality. However, the responses of root-associated bacteria to [CO2] elevation have not been characterized in a large-scale field study. We conducted a free-air CO2 enrichment (FACE) experiment (ambient + 200 µmol.mol(-1)) using three rice cultivars (Akita 63, Takanari, and Koshihikari) and two experimental lines of Koshihikari [chromosome segment substitution and near-isogenic lines (NILs)] to determine the effects of [CO2] elevation on the community structure of rice root-associated bacteria. Microbial DNA was extracted from rice roots at the panicle formation stage and analyzed by pyrosequencing the bacterial 16S rRNA gene to characterize the members of the bacterial community. Principal coordinate analysis of a weighted UniFrac distance matrix revealed that the community structure was clearly affected by elevated [CO2]. The predominant community members at class level were Alpha-, Beta-, and Gamma-proteobacteria in the control (ambient) and FACE plots. The relative abundance of Methylocystaceae, the major methane-oxidizing bacteria in rice roots, tended to decrease with increasing [CO2] levels. Quantitative PCR revealed a decreased copy number of the methane monooxygenase (pmoA) gene and increased methyl coenzyme M reductase (mcrA) in elevated [CO2]. These results suggest elevated [CO2] suppresses methane oxidation and promotes methanogenesis in rice roots; this process affects the carbon cycle in rice paddy fields.

Effect of paddy-upland rotation on methanogenic archaeal community structure in paddy field soil.

Methanogenic archaea are strict anaerobes and demand highly reduced conditions to produce methane in paddy field soil. However, methanogenic archaea survive well under upland and aerated conditions in paddy fields and exhibit stable community. In the present study, methanogenic archaeal community was investigated in fields where paddy rice (Oryza sativa L.) under flooded conditions was rotated with soybean (Glycine max [L.] Merr.) under upland conditions at different rotation histories, by polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) and real-time quantitative PCR methods targeting 16S rRNA and mcrA genes, respectively. Soil samples collected from the fields before flooding or seeding, during crop cultivation and after harvest of crops were analyzed. The abundance of the methanogenic archaeal populations decreased to about one-tenth in the rotational plots than in the consecutive paddy (control) plots. The composition of the methanogenic archaeal community also changed. Most members of the methanogenic archaea consisting of the orders Methanosarcinales, Methanocellales, Methanomicrobiales, and Methanobacteriales existed autochthonously in both the control and rotational plots, while some were strongly affected in the rotational plots, with fatal effect to some members belonging to the Methanosarcinales. This study revealed that the upland conversion for one or longer than 1 year in the rotational system affected the methanogenic archaeal community structure and was fatal to some members of methanogenic archaea in paddy field soil.