Culturable Populations of Sporomusa spp. and Desulfovibrio spp. in the Anoxic Bulk Soil of Flooded Rice Microcosms

Most-probable-number (MPN) counts were made of homoacetogenic and other bacteria present in the anoxic flooded bulk soil of laboratory microcosms containing 90- to 95-day-old rice plants. MPN counts with substrates known to be useful for the selective enrichment or the cultivation of homoacetogenic bacteria (betaine, ethylene glycol, 2,3-butanediol, and 3,4,5-trimethoxybenzoate) gave counts of 2.3 × 10³ to 2.8 × 10⁵ cells per g of dry soil. Homoacetogens isolated from the terminal positive steps of these dilution cultures belonged to the genus Sporomusa. Counts with succinate, ethanol, and lactate gave much higher MPNs of 5.9 × 10⁵ to 3.4 × 10⁷ cells per g of dry soil and led to the isolation of Desulfovibrio spp. Counting experiments on lactate and ethanol which included Methanospirillum hungatei in the medium gave MPNs of 2.3 × 10⁶ to 7.5 × 10⁸ cells per g of dry soil and led to the isolation of Sporomusa spp. The latter strains could grow with betaine, ethylene glycol, 2,3-butanediol, and/or 3,4,5-trimethoxybenzoate, but apparently most cells of Sporomusa spp. did not initiate growth in counting experiments with those substrates. Spores apparently accounted for 2.2% or less of the culturable bacteria. It appears that culturable Desulfovibrio spp. and Sporomusa spp. were present in approximately equal numbers in the bulk soil. Multiple, phylogenetically-distinct, phenotypically-different, strains of each genus were found in the same soil system.     

Characterization and identification of numerically abundant culturable bacteria from the anoxic bulk soil of rice paddy microcosms.

Most-probable-number (liquid serial dilution culture) counts were obtained for polysaccharolytic and saccharolytic fermenting bacteria in the anoxic bulk soil of flooded microcosms containing rice plants. The highest viable counts (up to 2.5 x 10(8) cells per g [dry weight] of soil) were obtained by using xylan, pectin, or a mixture of seven mono- and disaccharides as the growth substrate. The total cell count for the soil, as determined by using 4', 6-diamidino-2-phenylindole staining, was 4.8 x 10(8) cells per g (dry weight) of soil. The nine strains isolated from the terminal positive tubes in counting experiments which yielded culturable populations that were equivalent to about 5% or more of the total microscopic count population belonged to the division Verrucomicrobia, the Cytophaga-Flavobacterium-Bacteroides division, clostridial cluster XIVa, clostridial cluster IX, Bacillus spp., and the class Actinobacteria. Isolates originating from the terminal positive tubes of liquid dilution series can be expected to be representatives of species whose populations in the soil are large. None of the isolates had 16S rRNA gene sequences identical to 16S rRNA gene sequences of previously described species for which data are available. Eight of the nine strains isolated fermented sugars to acetate and propionate (and some also fermented sugars to succinate). The closest relatives of these strains (except for the two strains of actinobacteria) were as-yet-uncultivated bacteria detected in the same soil sample by cloning PCR-amplified 16S rRNA genes (U. Hengstmann, K.-J. Chin, P. H. Janssen, and W. Liesack, Appl. Environ. Microbiol. 65:5050-5058, 1999). Twelve other isolates, which originated from most-probable-number counting series indicating that the culturable populations were smaller, were less closely related to cloned 16S rRNA genes.     

Bacterial populations colonizing and degrading rice straw in anoxic paddy soil

Rice straw is a major substrate for the production of methane, a greenhouse gas, in flooded rice fields. The bacterial community degrading rice straw under anoxic conditions was investigated with molecular methods. Rice straw was incubated in paddy soil anaerobically for 71 days. Denaturing gradient gel electrophoresis (DGGE) of the amplified bacterial 16S rRNA genes showed that the composition of the bacterial community changed during the first 15 days but then was stable until the end of incubation. Fifteen DGGE bands with different signal intensities were excised, cloned, and sequenced. In addition, DNA was extracted from straw incubated for 1 and 29 days and the bacterial 16S rRNA genes were amplified and cloned. From these clone libraries 16 clones with different electrophoretic mobilities on a DGGE gel were sequenced. From a total of 31 clones, 20 belonged to different phylogenetic clusters of the clostridia, i.e., clostridial clusters I (14 clones), III (1 clone), IV (1 clone), and XIVa (4 clones). One clone fell also within the clostridia but could not be affiliated to one of the clostridial clusters. Ten clones grouped closely with the genera Bacillus (3 clones), Nitrosospira (1 clone), Fluoribacter (1 clones), and Acidobacterium (2 clones) and with clone sequences previously obtained from rice field soil (3 clones). The relative abundances of various phylogenetic groups in the rice straw-colonizing community were determined by fluorescence in situ hybridization (FISH). Bacteria were detached from the incubated rice straw with an efficiency of about 80 to 90%, as determined by dot blot hybridization of 16S rRNA in extract and residue. The number of active (i.e., a sufficient number of ribosomes) Bacteria detected with a general eubacterial probe (Eub338) after 8 days of incubation was 61% of the total cell counts. This percentage decreased to 17% after 29 days of incubation. Most (55%) of the active cells on day 8 belonged to the genus Clostridium, mainly to clostridial clusters I (24%), III (6%), and XIVa (24%). An additional 5% belonged to the Cytophaga-Flavobacterium cluster of the Cytophaga-Flavobacterium-Bacteroides phylum, 4% belonged to the alpha, beta, and gamma Proteobacteria, and 1.3% belonged to the Bacillus subbranch of the gram-positive bacteria with a low G+C content. The results show that the bacterial community colonizing and decomposing rice straw developed during the first 15 days of incubation and was dominated by members of different clostridial clusters, especially clusters I, III, and XIVa.     

Novel bacterial lineages at the (sub)division level as detected by signature nucleotide-targeted recovery of 16S rRNA genes from bulk soil and rice roots of flooded rice microcosms

Using a newly developed 16S rRNA gene (rDNA)-targeted PCR assay with proposed group specificity for planctomycetes, we examined anoxic bulk soil of flooded rice microcosms for the presence of novel planctomycete-like diversity. For comparison, oxic rice roots were included as an additional sample in this investigation. The bacterial diversity detectable by this PCR assay was assessed by using a combined approach that included terminal restriction fragment length polymorphism (T-RFLP) analysis and comparative sequence analysis of cloned 16S rDNA. T-RFLP fingerprint patterns generated from rice roots contained 12 distinct terminal restriction fragments (T-RFs). In contrast, the T-RFLP fingerprint patterns obtained from the anoxic bulk soil contained 33 distinct T-RFs, a clearly higher level of complexity. A survey of 176 bulk soil 16S rDNA clone sequences permitted correlation of 20 T-RFs with phylogenetic information. The other 13 T-RFs remained unidentified. The predominant T-RFs obtained from rice roots could be assigned to members of the genus Pirellula within the Planctomycetales, while most of the T-RFs obtained from the bulk soil corresponded to novel lines of bacterial descent. Using a level of 16S rDNA sequence dissimilarity to cultured microorganisms of approximately 20% as a threshold value, we detected 11 distinct bacterial lineages for which pure-culture representatives are not known. Four of these lineages could be assigned to the order Planctomycetales, while one lineage was affiliated with the division Verrucomicrobia and one lineage was affiliated with the spirochetes. The other five lineages either could not be assigned to any of the main lines of bacterial descent or clearly expanded the known diversity of division level lineages WS3 and OP3. Our results indicate the presence of bacterial diversity at a subdivision and/or division level that has not been detected previously by the so-called universal 16S rDNA PCR assays.     

Effects of freeze-thaw stress on bacterial populations in soil microcosms

To test the effect of freezing on soil biota, isolated from the shortgrass prairie of northeastern Colorado, a series of experiments were performed using gnotobiotic soil microcosms.Pseudomonas paucimobilis was used to examine the effects of freezing on bacteria of different growth stages. Secondly, the effect of multiple freeze-thaw cycles was tested on an assemblage of bacterial species. Lastly, the effect of freezing on predator-prey interactions was studied usingP. paucimobilis and an amoebal predator,Acanthamoeba polyphaga. A temperature of ?9°C was not detrimental toP. paucimobilis at any growth stage. A single severe freeze-thaw cycle (?27°C to 23°C) resulted in 40–60% mortality ofP. paucimobilis and the mixed bacteria, although additional freezing events did not reduce the populations further. Multiple freeze-thaw cycles (?9°C to 23°C) gave 40–60% mortality ofP. paucimobilis and the mixed bacteria. Predator-prey population cycles were possibly desynchronized by freeze-thaw events.     

Spatial distribution of methane-oxidizing activity in a flooded rice soil

In a study on spatial distribution of methane oxidation in an unplanted flooded field, methane-oxidizing activity, analysed in soil samples under laboratory conditions, decreased with increasing depth (25 cm and beyond). In a flooded field planted to rice, rates of methane oxidation followed the order : rhizosphere (collected from roots at 10-20 cm depth) > surface soil at (0-1 cm) > subsurface soil at 10-20 cm depth, diagonally 10-15 cm away from the centre of hill. Application of ammonium sulfate and, to a lesser extent, urea to surface, rhizosphere and subsurface soil samples from flooded field planted to rice effected a distinct inhibition of methane oxidation. Nitrification inhibitors (thiourea, sodium thiosulfate and dicyandiamide) were also effective in inhibiting methane oxidation. Both surface and rhizosphere soil samples harbored higher populations of methane-oxidizing bacteria than the subsurface soil. Inhibition of methane oxidation in surface and rhizosphere soil samples concomitant with the suppression of autotrophic ammonium oxidizers by nitrification inhibitors implicates an active involvement of autotrophic ammonium oxidizers in methane oxidation.     

Absorption of molecular urea by rice under flooded and non-flooded soil conditions

A pot experiment was conducted with rice to study the relative absorption of urea in molecular form compared to the other forms of N produced in soil from the applied urea. A method involving application of ¹⁴C-labelled urea and ¹⁵N-labelled urea alternately in two splits was used to quantify the absorption of molecular urea and other forms of N formed from it. Biomass production and N uptake were greater in plants grown under flooded soil conditions than in plants grown under non-flooded (upland) conditions. Absorption of N by rice increased with increasing rate of urea application up to 250 mg pot⁻¹ and declined thereafter. The absorption of urea from the flooded soil constituted 9.4% of total N uptake from applied N compared to only 0.2% from the non-flooded. Under submerged conditions, absorption of urea from topdressing was about twice that from basal application at planting. High water solubility of the fertilizer and better developed rice root system might have enhanced the absorption of molecular urea by flooded rice, especially from topdressing. Thus, in the flooded rice system, the direct absorption of molecular urea from topdressing accounted for 6.3% of the total N uptake from added urea. Under upland condition, it was 0.12%. This revised version was published online in June 2006 with corrections to the Cover Date.     

Sporomusa,a new genus of gram-negative anaerobic bacteria including Sporomusa sphaeroides spec. nov. and Sporomusa ovata spec. nov.

A new genus of strictly anaerobic, gram-negative, banana-shaped bacteria is described. Cells formed spores and were motile by means of up to 15 laterally inserted flagella. Nitrate or sulfate were not used as electron acceptor. Organic substrates that were fermented included N-methyl compounds, such as betaine, N,N-dimethylglycine and sarcosine, primary alcohols, hydroxy fatty acids, and 2,3-butanediol. In addition, molecular hydrogen and carbon dioxide were fermented to acetate. The latter was the characteristic fermentation product in general. During growth on betaine, trimethylamine was formed in addition. The degradation of N,N-dimethylglycine yielded acetate, monomethylamine, and trimethylamine. The presence of cytochrome b and of ubiquinone in the cells was shown. The deoxyribonuleic acid base composition of the strains was between 41.3 and 47.4 mol% guanine plus cytosine. The name Sporomusa is proposed for this new genus. On the basis of the DNA-DNA homology values obtained, the shape of the spores and some other properties, the isolated strains were assigned to two species. Names proposed: Sporomusa sphaeroides and Sporomusa ovata. The type species is S. sphaeroides and the type strains are strain E, DSM 2875 (S. sphaeroides) and strain H1, DSM 2662 (S. ovata).Dedicated to Prof. H. G. Schlegel on the occasion of his 60th birthday     

Comparative bioenergetics of sulfate reduction in Desulfovibrio and Desulfotomaculum spp.

Extracts of Desulfotomaculum nigrificans, Desulfotomaculum orientis, and Desulfotomaculum ruminis exhibit low levels of inorganic pyrophosphatase but were found to have high levels of pyrophosphate:acetate phosphotransferase. Conversely, extracts of Desulfovibrio gigas, Desulfovibrio vulgaris, and Desulfovibrio desulfuricans Norway 4 were shown to have high levels of inorganic pyrophosphatase but negligible amounts of pyrophosphate:acetate phosphotransferase. Both enzymes are reductant activated and appear to have an analogous function in removing pyrophosphate formed during the activation of sulfate. Conservation of the bond energy of pyrophosphate in Desulfotomaculum eliminates the necessity for invoking electron-transfer-coupled phosphorylation to account for the growth of these bacteria on lactate plus sulfate. Relative growth yields of Desulfovibrio vulgaris and Desulfotomaculum orientis on lactate plus sulfate indicate that the latter does not carry out significant electron-transfer-coupled phosphorylation in this mode of growth.     

Pattern of non-methanogenic and methanogenic degradation of cellulose in anoxic rice field soil

Rice field soils turn anoxic upon flooding. The complete mineralization of organic matter, e.g. cellulose, to gaseous products is then accomplished by the sequential reduction of nitrate, ferric iron, sulfate and finally by methanogenesis. Therefore, the anaerobic turnover of [U-(14)C]cellulose was investigated in fresh, non-methanogenic and in preincubated, methanogenic slurries of Italian rice field soil. In anoxic soil slurries freshly prepared from air-dried soil [U-(14)C]cellulose was converted to (14)CO(2) and (14)CH(4) in a ratio of 3:1. In methanogenic soil slurries, on the other hand, which had been preincubated for 45 days under anaerobic conditions, [U-(14)C]cellulose was converted to (14)CO(2) and (14)CH(4) in the ratio of 1:1. The turnover times (7-14 days) of cellulose degradation were not significantly different (P0.05) in fresh and methanogenic soil. Chloroform addition abolished CH(4) production, but only slightly (30%) inhibited cellulose degradation in both fresh and methanogenic soil. Under both soil conditions, [(14)C]acetate was the only labeled intermediate detected. A maximum of 24% of the applied radioactivity was transiently accumulated as [(14)C]acetate in both fresh and methanogenic soil slurries. However, when methanogenesis was inhibited by chloroform, 46% and 66% of the applied radioactivity were recovered as [(14)C]acetate in fresh and methanogenic soil, respectively. Only non-radioactive propionate accumulated during the incubation with [U-(14)C]cellulose, especially in the presence of chloroform, indicating that propionate was produced from substrates other than cellulose.     

Effect of soil aggregate size on methanogenesis and archaeal community structure in anoxic rice field soil

In anoxically incubated slurries of Italian rice field soil, CH(4) production is initiated after a lag phase during which ferric iron and sulfate are reduced. The production of CH(4) was affected by the size of soil aggregates used for the preparation of the soil slurry. Rates of CH(4) production were lowest with small aggregates (<50 and 50-100 μm), were highest with aggregates of 200-2000 μm size and were intermediate with aggregates of 2000-15000 μm size. The different amounts of CH(4) accumulated were positively correlated to the concentrations of acetate, propionate and caproate that transiently accumulated in the slurries prepared from different aggregate sizes and also to the organic carbon content. The addition of organic debris that was collected from large-size aggregates to the aggregate size fractions <200 and <50 μm resulted in an increase of CH(4) production to amounts that were comparable to those measured in unamended aggregates of 200-2000 μm size, indicating that CH(4) production in the different aggregate size fractions was limited by substrate. The distribution of archaeal small-subunit rRNA genes in the different soil aggregate fractions was analyzed by terminal restriction fragment length polymorphism which allowed seven different archaeal ribotypes to be distinguished. Ribotype-182 (consisting of members of the Methanosarcinaceae and rice cluster VI), ribotype-389 (rice cluster I and II) and ribotype-820 (undigested DNA, rice cluster IV and members of the Methanosarcinaceae) accounted for >20, >30 and >10% of the total, respectively. The other ribotypes accounted for <10% of the total. The relative quantity of the individual ribotypes changed only slightly with incubation time and was almost the same among the different soil aggregate fractions. Ribotype-389, for example, slightly decreased with time, whereas ribotype-182 slightly increased. At the end of incubation, the relative quantity of ribotype-182 seemed to be slightly higher in soil fractions with larger than with smaller aggregates, whereas it was the opposite with ribotype-80 (Methanomicrobiaceae) and ribotype-88 (Methanobacteriaceae). Ribotype-280 (Methanosaetaceae and rice cluster V), ribotype-375 (rice cluster III), ribotype-389 and ribotype-820, on the other hand, were not much different among the different soil aggregate size fractions. However, the differences were not significant relative to the errors encountered during the extraction of polymerase chain reaction (PCR)-amplifiable DNA from soil. In conclusion, soil aggregate size and incubation time showed a strong effect on the function but only a small effect on the structure of the methanogenic microbial community.     

Contribution of plant photosynthates to dissolved organic carbon in a flooded rice soil

Dissolved organic C (DOC) plays important roles in nutrient cycling and methane production in flooded rice ecosystem. The microcosm experiment was carried out to measure directly the contribution of photosynthates to DOC by using a ¹³C pulse-chase labeling technique. DOC was operationally divided into water-extractable organic C (WEOC) and salt-extractable organic C (SEOC) by successive extraction firstly with deionized water and then with 0.25 M K₂SO₄. Total WEOC increased with plant growth, whereas SEOC concentration did not change significantly over the growing season. About 0.037–0.36% (mean 0.16%) of the assimilated ¹³C was incorporated into WEOC immediately after ¹³CO₂ assimilation (Day 0), but only 0–0.025% (mean 0.01%) was incorporated into SEOC. At the end of the growing season, the ¹³C amounts of WEOC substantially decreased, while those of SEOC slightly increased. The estimated net plant C contribution was 21 mg C plant^–1 to WEOC and 6 mg C plant^–1 to SEOC, corresponding to 33.8% of total WEOC and 20.2% of total SEOC at the end of the growing season, respectively. The results suggest that the incorporation and decomposition of the photosynthesized C occurred rapidly in rice soil which significantly affected the WEOC dynamics, but SEOC appeared to be in equilibrium with the native soil organic matter, receiving less effect from the plant growth.     

Fermentation pattern of methanogenic degradation of rice straw in anoxic paddy soil

The anaerobic degradation of different fractions of rice straw in anoxic paddy soil was investigated. Rice straw was divided up into stem, leaf sheath and leaf blade. The different straw fractions were mixed with paddy soil and incubated under anoxic conditions. Fermentation of straw components started immediately and resulted in transient accumulation of acetate, propionate, butyrate, isobutyrate, valerate, isovalerate and caproate with much higher concentrations in the presence than in the absence of straw. Also some unidentified compounds with UV absorption could be detected. The maximum concentrations of these compounds were different when using different straw fractions, suggesting differences in the degradation pathway of these straw fractions during the early phase of incubation, i.e. with Fe(III) and sulfate serving as oxidants. When concentrations of the intermediates decreased to background values, CH(4) production started. Rates of CH(4)unamended soil. During the methanogenic phase, the percentage contribution of fermentation products to CH(4) production was determined by inhibition with 2-bromoethanesulfonate (BES). Acetate (48-83%) and propionate (18-28%) were found to be the main intermediates of the carbon flow to CH(4), irrespective of the fraction of the rice straw or its absence. Mass balance calculations showed that 84-89% of CH(4) was formed via acetate in the various incubations. Radiotracer experiments showed that 11-27% of CH(4) was formed from H(2)/CO(2), thus confirming that acetate contributed 73-89% to methanogenesis. Our results show that the addition of rice straw and the fraction of the straw affected the fermentation pattern only in the early phase of degradation, but had no effect on the degradation pathway during the later methanogenic phase.     

Mineralization budgets in sediment microcosms: Effect of the infauna and anoxic conditions

Abstract A number of sediment incubations were set up to reproduce some of the conditions used by Kristensen and Blackburn [1] and to make a comparison with their results. There were three types of microcosm: aerobic (OX), anaerobic (AN) and aerobic with Nephtys (NOX). In addition to other measurements, dissolved organic nitrogen (DON) pools and fluxes, were measured. The sediment in this experiment contained more particulate organic matter (POM). Nephtys (NOX) had the same effect as Nereis in increasing the rate of mineralization of POC and PON, compared with the OX-cores (2.1 and 2.6 times, respectively). Again, the AN-cores had a higher mineralization rate (loss of POM) than that of the OX-cores, but in addition, mineralization in NOX-cores was not significantly different from AN-cores. It was thus confirmed that anoxic mineralization could be as high, or higher, than the oxic process. Both the temporal patterns of O₂-and and CO₂-fluxes and their magnitudes were very similar to those reported earlier. This contrasts with the higher loss of POM in the present experiment. However, the loss of C in DOC (associated with the measured DON) can account for the extra POM loss. The pore-water profiles of σCO₂ and NH₄⁺ were similar to those in the earlier report, and the fluxes of σCO₂, O₂, NH₄⁺ and NO₃⁻ followed the same temporal pattern.     

Effect of temperature on structure and function of the methanogenic archaeal community in an anoxic rice field soil.

Soil temperatures in Italian rice fields typically range between about 15 and 30 degrees C. A change in the incubation temperature of anoxic methanogenic soil slurry from 30 degrees C to 15 degrees C typically resulted in a decrease in the CH4 production rate, a decrease in the steady-state H2 partial pressure, and a transient accumulation of acetate. Previous experiments have shown that these changes were due to an alteration of the carbon and electron flow in the methanogenic degradation pathway of organic matter caused by the temperature shift (K. J. Chin and R. Conrad, FEMS Microbiol. Ecol. 18:85-102, 1995). To investigate how temperature affects the structure of the methanogenic archaeal community, total DNA was extracted from soil slurries incubated at 30 and 15 degrees C. The archaeal small-subunit (SSU) rRNA-encoding genes (rDNA) of these environmental DNA samples were amplified by PCR with an archaeal-specific primer system and used for the generation of clone libraries. Representative rDNA clones (n = 90) were characterized by terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis. T-RFLP analysis produced for the clones terminally labeled fragments with a characteristic length of mostly 185, 284, or 392 bp. Sequence analysis allowed determination of the phylogenetic affiliation of the individual clones with their characteristic T-RFLP fragment lengths and showed that the archaeal community of the anoxic rice soil slurry was dominated by members of the families Methanosarcinaceae (185 bp) and Methanosaetaceae (284 bp), the kingdom Crenarchaeota (185 or 284 bp), and a novel, deeply branching lineage of the (probably methanogenic) kingdom Euryarchaeota (392 bp) that has recently been detected on rice roots (R. Grosskopf, S. Stubner, and W. Liesack, Appl. Environ. Microbiol. 64:4983-4989, 1998). The structure of the archaeal community changed when the temperature was shifted from 30 degrees C to 15 degrees C. Before the temperature shift, the clones (n = 30) retrieved from the community were dominated by Crenarchaeota (70%), "novel Euryarchaeota" (23%), and Methanosarcinacaeae (7%). Further incubation at 30 degrees C (n = 30 clones) resulted in a relative increase in members of the Methanosarcinaceae (77%), whereas further incubation at 15 degrees C (n = 30 clones) resulted in a much more diverse community consisting of 33% Methanosarcinaceae, 23% Crenarchaeota, 20% Methanosaetaceae, and 17% novel Euryarchaeota. The appearance of Methanosaetaceae at 15 degrees C was conspicuous. These results demonstrate that the structure of the archaeal community in anoxic rice field soil changed with time and incubation temperature.     

Contribution of plant photosynthates to dissolved organic carbon in a flooded rice soil

Dissolved organic C (DOC) plays important roles in nutrient cycling and methane production in flooded rice ecosystem. The microcosm experiment was carried out to measure directly the contribution of photosynthates to DOC by using a ¹³C pulse-chase labeling technique. DOC was operationally divided into water-extractable organic C (WEOC) and salt-extractable organic C (SEOC) by successive extraction firstly with deionized water and then with 0.25?M K₂SO₄. Total WEOC increased with plant growth, whereas SEOC concentration did not change significantly over the growing season. About 0.037–0.36% (mean 0.16%) of the assimilated ¹³C was incorporated into WEOC immediately after ¹³CO₂ assimilation (Day 0), but only 0–0.025% (mean 0.01%) was incorporated into SEOC. At the end of the growing season, the ¹³C amounts of WEOC substantially decreased, while those of SEOC slightly increased. The estimated net plant C contribution was 21?mg?C?plant^?1 to WEOC and 6?mg?C?plant^?1 to SEOC, corresponding to 33.8% of total WEOC and 20.2% of total SEOC at the end of the growing season, respectively. The results suggest that the incorporation and decomposition of the photosynthesized C occurred rapidly in rice soil which significantly affected the WEOC dynamics, but SEOC appeared to be in equilibrium with the native soil organic matter, receiving less effect from the plant growth.     

Effect of rice straw additions on production of organic acids in a flooded soil

Summary Disposal of rice straw through soil incorporation may contribute to anaerobic fermentation processes producing concentrations of organic acids which are toxic to rice plants. The present studies were conducted to determine the kind, amount, and time of production of organic acids as a function of rice straw additions (0, 0.25, and 0.5 per cent of soil weight), and temperature (10, 20, and 30°C). Nine samples were taken at 5, and 10 day intervals for 60 days to measure concentrations of organic acids.Only acetic acid was detected in the incubated soil with rice straw added. The amount and peak production of acetic acid increased with the rate of straw added and temperature. Acetic acid concentrations varied between 10.6 and 22.7 eq/20 g soil, and the peak production occurred between 15 and 20 days after incubation. Organic acids were not found in sufficient amounts to affect the growth of rice plants grown in soils that were not previously puddled or in a reduced state.Contribution from the Department of Agronomy and Range Science, University of California, Davis, California 95616.Contribution from the Department of Agronomy and Range Science, University of California, Davis, California 95616.     

Localization of processes involved in methanogenic degradation of rice straw in anoxic paddy soil

In anoxic paddy soil, rice straw is decomposed to CH(4) and CO(2) by a complex microbial community consisting of hydrolytic, fermenting, syntrophic and methanogenic microorganisms. Here, we investigated which of these microbial groups colonized the rice straw and which were localized in the soil. After incubation of rice straw in anoxic soil slurries for different periods, the straw pieces were removed from the soil, and both slurry and straw were studied separately. Although the potential activities of polysaccharolytic enzymes were higher in the soil slurry than in the straw incubations, the actual release of reducing sugars was higher in the straw incubations. The concentrations of fermentation products, mainly acetate and propionate, increased steadily in the straw incubations, whereas only a little CH(4) was formed. In the soil slurries, on the other hand, fermentation products were low, whereas CH(4) production was more pronounced. The production of CH(4) or of fermentation products in the separated straw and soil incubations accounted in sum for 54-82% of the CH(4) formed when straw was not removed from the soil. Syntrophic propionate degradation to acetate, CO(2) and H(2) was thermodynamically more favourable in the soil than in the straw fraction. These results show that hydrolysis and primary fermentation reactions were mainly localized on the straw pieces, whereas the syntrophic and methanogenic reactions were mainly localized in the soil. The percentage of bacterial relative to total microbial 16S rRNA content was higher on the straw than in the soil, whereas it was the opposite for the archaeal 16S rRNA content. It appears that rice straw is mainly colonized by hydrolytic and fermenting bacteria that release their fermentation products into the soil pore water where they are further degraded to CH(4). Hence, complete methanogenic degradation of straw in rice soil seems to involve compartmentalization.