Rice roots select for type I methanotrophs in rice field soil

Methanotrophs are an important regulator for reducing methane (CH₄) emissions from rice field soils. The type I group of the proteobacterial methanotrophs are generally favored at low CH₄ concentration and high O₂ availability, while the type II group lives better under high CH₄ and limiting O₂ conditions. Such physiological differences are possibly reflected in their ecological preferences. In the present study, methanotrophic compositions were compared between rice-planted soil and non-planted soil and between the rhizosphere and rice roots by using terminal restriction fragment length polymorphism (T-RFLP) analysis of particulate methane monooxygenase (pmoA) genes. In addition, the effects of rice variety and nitrogen fertilizer were evaluated. The results showed that the terminal restriction fragments (T-RFs), which were characteristic for type I methanotrophs, substantially increased in the rhizosphere and on the roots compared with non-planted soils. Furthermore, the relative abundances of the type I methanotroph T-RFs were greater on roots than in the rhizosphere. Of type I methanotrophs, the 79 bp T-RF, which was characteristic for an unknown group or Methylococcus/Methylocaldum, markedly increased in field samples, while the 437 bp, which possibly represented Methylomonas, dominated in microcosm samples. These results suggested that type I methanotrophs were enriched or selected for by rice roots compared to type II methanotrophs. However, the members of type I methanotrophs are dynamic and sensitive to environmental change. Rice planting appeared to increase the copy number of pmoA genes relative to the non-planted soils. However, neither the rice variety nor the N fertilizer significantly influenced the dynamics of the methanotrophic community.     

Isolation and molecular characterization of thiosulfate-oxidizing bacteria from an Italian rice field soil

In rice paddy soils an active cycling of sulfur compounds takes place. To elucidate the diversity of thiosulfate-oxidizing bacteria these organisms were enriched from bulk soil and rice roots by the most probable number method in liquid medium. From the MPN enrichment cultures 21 bacterial strains were isolated on solid mineral medium, and could be further shown to produce sulfate from thiosulfate. These strains were characterized by 16S rDNA analyses. The isolates were affiliated to seven different phylogenetic groups within the alpha- and beta-subclass of Proteobacteria. Two of these phylotypes were already described as S-oxidizers in this environment (Xanthobacter sp. and Bosea sp. related strains), but five groups represented new S-oxidizers in rice field soil. These isolates were closely related to Mesorhizobium loti, to Hydrogenophaga sp., to Delftia sp., to Pandoraea sp. or showed sequence similarity to a strain of Achromobacter sp.     

Allelochemicals released by rice roots and residues in soil

A few rice (Oryza sativa L.) varieties or rice straw produce and release allelochemicals into soil in which interfere with the growth of neighboring or successive plants. Allelopathic rice PI312777 and Huagan-1 at their early growth stages released momilactone B, 3-isopropyl-5-acetoxycyclohexene-2-one-1, and 5,7,4′-trihydroxy-3′,5′-dimethoxyflavone into soil at phytotoxic levels, but non-allelopathic rice Huajingxian did not. Both allelopathic and non-allelopathic rice residues released momilactone B and lignin-related phenolic acids (p-hydroxybenzoic, p-coumaric, ferulic, syringic and vanillic acids) into the soil during residue decomposition to inhibit successive plants. The results indicated that allelochemicals involved in rice allelopathy from living and dead plants are substantially different. Interestingly, the concentrations of the allelochemicals released from the allelopathic rice seedlings in soil increased dramatically when they were surrounded with Echinochloa crus-galli. The concentrations of the allelochemicals were over 3-fold higher in the presence of E. crus-galli than in the absence of E. crus-galli. However, the same case did not occur in non-allelopathic Huajingxian seedlings surrounded with E. crus-galli. In addition to allelochemical exudation being promoted by the presence of E. crus-galli, allelopathic rice seedlings also increased allelochemical exudation in response to exudates of germinated E. crus-galli seeds or lepidimoide, an uronic acid derivative exuded from E. crus-galli seeds. These results imply that allelopathic rice seedlings can sense certain allelochemicals released by E. crus-galli into the soil, and respond by increased production of allelochemicals inhibitory to E. crus-galli. This study suggests that rice residues of both allelopathic and non-allelopathic varieties release similar concentrations and types of allelochemicals to inhibit successive plants. In contrast, living rice plants of certain allelopathic varieties appear to be able to detect the presence of interspecific neighbors and respond by increased allelochemicals.     

Thermophilic methanogens in rice field soil

The soil temperature in flooded Italian rice fields is generally lower than 30°C. However, two temperature optima at ≈ 41°C and 50°C were found when soil slurries were anoxically incubated at a temperature range of 10–80°C. The second temperature optimum indicates the presence of thermophilic methanogens in the rice field soil. Experiments with ¹⁴C-labelled bicarbonate showed that the thermophilic CH₄ was exclusively produced from H₂/CO₂. Terminal restriction fragment length polymorphism (T-RFLP) of archaeal SSU rRNA gene fragments revealed a dramatic change in the archaeal community structure at temperatures > 37°C, with the euryarchaeotal rice cluster I becoming the dominant group (about 80%). A clone library of archaeal SSU rRNA gene fragments generated at 49°C was also dominated (10 out of 11 clones) by rice cluster I. Our results demonstrate that Italian rice field soil contains thermophilic methanogenic activity that was most probably a result of members of the as yet uncultivated euryarchaeotal rice cluster I.     

Community composition of ammonia-oxidizing bacteria and archaea in rice field soil as affected by nitrogen fertilization

Little information is available on the ecology of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in flooded rice soils. Consequently, a microcosm experiment was conducted to determine the effect of nitrogen fertilizer on the composition of AOB and AOA communities in rice soil by using molecular analyses of ammonia monooxygenase gene (amoA) fragments. Experimental treatments included three levels of N (urea) fertilizer, i.e. 50, 100 and 150 mg N kg⁻¹ soil. Soil samples were operationally divided into four fractions: surface soil, bulk soil deep layer, rhizosphere and washed root material. NH₄⁺-N was the dominant form of N in soil porewater and increased with N fertilization. Cloning and sequencing of amoA gene fragments showed that the AOB community in the rice soil consisted of three major groups, i.e. Nitrosomonas communis cluster, Nitrosospira cluster 3a and cluster 3b. The sequences related to Nitrosomonas were predominant. There was a clear effect of N fertilizer and soil depth on AOB community composition based on terminal restriction fragment length polymorphism fingerprinting. Nitrosomonas appeared to be more abundant in the potentially oxic or micro-oxic fractions, including surface soil, rhizosphere and washed root material, than the deep layer of anoxic bulk soil. Furthermore, Nitrosomonas increased relatively in the partially oxic fractions and that of Nitrosospira decreased with the increasing application of N fertilizer. However, AOA community composition remained unchanged according to the denaturing gradient gel electrophoresis analyses.     

Sulfate-reducing bacteria in littoral sediment of Lake Constance

Abstract The viable population of sulfate-reducing bacteria (SRB) in littoral sediments of Lake Constance was investigated using enrichment and enumeration techniques. Enrichment studies established that most types of SRB grew best in media with low salt concentrations (max. 0.4 g Cl⁻/1), consistent with the low salinity of the freshwater habitat. Enumerations were based on an adequate medium with the following electron donors: H₂, lactate, acetate, propionate, butyrate, caprylate, succinate, benzoate, or S₂O₃²⁻ for thiosulfate-disproportionating bacteria. Cultures were incubated for 6 weeks to obtain maximum counts. A maximum cell density of 6.3 × 10⁶ cells per ml sediment was estimated, which is the highest number of SRB ever reported for anoxic sediments. A comparison with measured sulfate reduction rates showed that the enumeration techniques were about 10–100-fold more efficient than those previously used. The population of SRB had a characteristic structure consisting of 87.7% H₂-utilizing SRB (physiologically resembling the classical Desulfovibrio species); 12.0% propionate utilizers (tentatively identified as Desulfobulbus species); 0.3% long chain fatty acid-oxidizing Desulfovibrio sapovorans species. Acetate-utilizing SRB ( Desulfotomaculum acetoxidans ) constituted ≤ 0.05% of the total estimated population. Moreover, the latter species was only present as inactive spores. Benzoate-degrading SRB were not detected.     

Effect of soil temperature on nitrogen fixation on roots of rice and reed

Summary The relation of nitrogenase activity (ethylene evolution) to soil temperature or incubation temperature of roots was determined on two genera of swamp plants, namely rice (Oryza sativa) cultivated in tropical climate and reed (Phragmites communis) grown in temperate regions. For both intact rice plants and excised rice roots the optimum temperature was 35°C. On excised roots nitrogenase activity responded more sensitivity to changes in temperature. In contrast to intact rice plants no ethylene evolution occurred on excised roots at 17 and 44°C. On reed roots temperature optimum was between 26 and 30°C which is clearly lower than on rice (35°C). The temperature range in which nitrogen fixation occurred was, however, similar to that of rice, although on a lower level. The results suggest a higher potential of the tropics for associative N₂ fixation, while in cooler climates the lower temperatures appear to be a major limiting factor.     

Quantification of Gram-negative sulphate-reducing bacteria in rice field soil by 16S rRNA gene-targeted real-time PCR

For the quantification of Gram-negative sulphate reducers in rice fields, 11 real-time PCR assays were established targeting 16S rRNA genes combined with SybrGreen detection. Three of these assays were specific for the "main" groups, i.e. the Desulfovibrionaceae, the Desulfobacteraceae and Desulfobulbus sp., whereas eight assays were developed for subgroups within the first two main groups. The detection limits of the assays were between 2 x 10(5) and 4 x 10(3) targets g(-1) (wet weight) or less than 0.02% of the eubacterial 16S rDNA targets in bulk soil, rhizosphere soil and rice root DNA extracts. Analysis of soil spiked with defined cell numbers of sulphate-reducing bacteria showed good correlation of measured target numbers to amended cells. In rice field bulk and rhizosphere soil, the Desulfobacteraceae were the predominant main group with target numbers of 6.4 x 10(7) (+/-1.0 x 10(7)) and 7.5 x 10(7) (+/-1.7 x 10(7)), respectively. Within this group the Desulforhabdus/Synthrophobacter assemblage and Desulfobacterium sp. were predominant. At the rice roots, the three main groups were abundant in similar numbers (approx. 1.0 x 10(8)) indicating that the relative abundance of the Desulfovibrionaceae and also of Desulfobulbus sp. was increased, relatively to the Desulfobacteraceae. Within the Desulfovibrionaceae the subgroup was predominant that was detected by assay DSV-II. This assay detects many from rice field soil isolated Desulfovibrio-strains and molecular retrieved sequences. Therefore these organisms that were already detected in the rice field environment by isolation and by molecular techniques are indeed best adapted to the conditions provided by the rice roots.     

Sulfate-reducing bacteria in gypsum karst lakes of northern Lithuania

Microbiological studies were performed in three small gypsum karst lakes in northern Lithuania, most typical of the region. Samples were taken in different seasons of 2001. The conditions for microbial growth in the lakes are determined by elevated content of salts (from 0.5 to 2.0 g/l), dominated by SO(2-)4 and Ca2+ ions (up to 1.4 and 0.6 g/l, respectively). The elevated sulfate concentration is favorable for sulfate-reducing bacteria (SRBs). Summer and winter stratification gives rise to anaerobic water layers enriched in products of anaerobic degradation: H2S and CH4. The lakes under study contain abundant SRBs not only in bottom sediments (from 10(3) to 10(7) cells/dm3) but also in the water column (from 10(2) to 10(6) cells/ml). The characteristic spatial and temporal variations in the rate of sulfate reduction were noted. The highest rates of this process were recorded in summer: 0.95-2.60 mg S(2-)/dm3 per day in bottom sediments and up to 0.49 mg S(2-)/l per day in the water column. The maximum values (up to 11.36 mg S(2-)/dm3) were noted in areas where bottom sediments were enriched in plankton debris. Molecular analysis of conservative sequences of the gene for 16S RNA in sulfate-reducing microorganisms grown on lactate allowed them to be identified as Desulfovibrio desulfuricans.     

Microbial mechanism for rice variety control on methane emission from rice field soil

Rice variety is one of the key factors regulating methane (CH₄) production and emission from the paddy fields. However, the relationships between rice varieties and populations of microorganisms involved in CH₄ dynamics are poorly understood. Here we investigated CH₄ dynamics and the composition and abundance of CH₄‐producing archaea and CH₄‐oxidizing bacteria in a Chinese rice field soil planted with three types of rice. Hybrid rice produced 50–60% more of shoot biomass than Indica and Japonica cultivars. However, the emission rate of CH₄ was similar to Japonica and lower than Indica. Furthermore, the dissolved CH₄ concentration in the rhizosphere of hybrid rice was markedly lower than Indica and Japonica cultivars. The rhizosphere soil of hybrid rice showed a similar CH₄ production potential but a higher CH₄ oxidation potential compared with the conventional varieties. Terminal restriction fragment length polymorphism analysis of the archaeal 16S rRNA genes showed that the hydrogenotrophic methanogens dominated in the rhizosphere whereas acetoclastic methanogens mainly inhabited the bulk soil. The abundance of total archaea as determined by quantitative (real‐time) PCR increased in the later stage of rice growth. However, rice variety did not significantly influence the structure and abundance of methanogenic archaea. The analysis of pmoA gene fragments (encoding the α‐subunit of particulate methane monooxygenase) revealed that rice variety also did not influence the structure of methanotrophic proteobacteria, though variable effects of soil layer and sampling time were observed. However, the total copy number of pmoA genes in the rhizosphere of hybrid rice was approximately one order of magnitude greater than the two conventional cultivars. The results suggest that hybrid rice stimulates the growth of methanotrophs in the rice rhizosphere, and hence enhances CH₄ oxidation which attenuates CH₄ emissions from the paddy soil. Hybrid rice is becoming more and more popular in Asian countries. The present study demonstrated that planting of hybrid rice will not enhance CH₄ emissions albeit a higher grain production than the conventional varieties.     

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.     

Enrichment of diazotrophic bacteria from rice soil in continuous culture

Summary A chemostat was used as a model system to study competitive interactions of diazotrophic microorganisms. Enrichment experiments were carried out under microaerobic conditions (8.7 mol O₂/l) with malate as the sole carbon source. The starting material was a Korean rice soil including intact root pieces. The enrichment process was governed by the dilution rate. High dilution rates resulted in the enrichment ofAzospirillum lipoferum, whereas low dilution rates led to the predominance of an unidentified organism, named Isolate R. Dilution rates were set in the range from D=0.005 to D=0.1 h^–1. The growth kinetics of both organisms followed Monod's model in the enrichment culture. From the experiments, the maximum specific growth rate ofA. lipoferum and Isolate R were 0.069 h^–1 and 0.025 h^–1, respectively. The corresponding K_s-values were 8.4 and 0.9 (mg. 1^–1). The point of theoretical coexistence of both organisms was calculated to occur at a substrate concentration of s=3.0 (mg.l^–1) with a growth of rate =0.018 h^–1. Hence the preset nutritional niches occupied by at least two organisms.Azospirillum lipoferum seems to represent the copiotroph microflora and Isolate R is of the oligotroph type. In addition to its high substrate affinity Isolate R liberatedca. 75% of the fixed nitrogen into the medium, which indicates its potential role for mutualistic interactions in the rhizosphere.     

Localization of sulfate reduction in planted and unplanted rice field soil

Rates of in situ sulfate reduction (SRR) in planted and unplanted rice fieldsoil were measured by the ³⁵SO^2– ₄-radiotracermethod using soil microcosms. The concentration of ³⁵SO^2– ₄ decreased exponentially with time.However, time course experiments indicated that incubation times of10–30 min were appropriate for measurements of SRRusing a single time point in routine assays. Unplanted microcosmsshowed high SRR of 177 nmol cm^-3 d^-1 inthe uppermost centimeter where average sulfate concentrations were<33 µM. Fine scaled measurements (1 mmresolution) localized highest SRR (<100 nmol cm^-3d^-1) at the oxic/anoxic interface at 2–5 mmdepth. In planted rice field soil, SRR of <310 nmolcm^-3 d^-1 were observed at 0–2cm depth. Sulfate reduction rates were determined at a millimeter-scalewith distance to a two dimensional root compartment. The SRR was highestat 0–1.5 mm distance to the root layer with rates up to500 nmol cm^-3 d^-1, indicating a highstimulation potential of the rice roots. SRR seemed to be mainlydependent on the in situ sulfate porewater concentrations. At thesoil surface of unplanted microcosms sulfate concentration decreasedfrom <150 µM to <10 µM within the first 8 mm of depth. In planted microcosmssulfate concentration varied from 87–99 µMsulfate at the 0–3 mm distance to the root layer to48–62 µM sulfate at a root distance>4 mm from the roots.The depth distribution of inorganic sulfur compounds was determinedfor planted and unplanted rice field soil. Sulfate, acid volatilesulfide (AVS) and chromium reducible sulfide (CRS) were up to 20 foldhigher in planted than in unplanted microcosms. CRS was the majorinsoluble sulfur fraction with concentrations >1.7µmol cm^-3. Organic sulfur accounted for25–46% of the total sulfurpresent (269 µg/g dw) in an unplanted microcosm.The biogeochemical role of sulfate reduction forshort-term accumulation of inorganic sulfur compounds(FeS, FeS_{_2} and S°) in rice soil wasdetermined in a time course experiment with incubationperiods of 5, 10, 20, 30 and 60 min. The relativedistribution of CRS and AVS formation showedlittle depth dependence, whereas the formation of³⁵S° seemed to be the highest in themore oxidized upper soil layers and near the root surface.AV³⁵S was the first major product of sulfatereduction after 20–30 min, whereas CR³⁵Swas formed, as AV³⁵S and ³⁵S°decreased, at longer incubation periods of >30 min.     

蒙古栎根内及根围土壤中共生真菌和细菌群落组成分析

为探究中国东北地区森林根系和根围土壤中共生真菌的分布状况,分析了黑龙江省五大连池市蒙古栎Quercus mongolica纯林中根内及根围土壤中共生真菌和细菌群落的组成。结果表明,根内真菌的1 295个OTUs中有209个OTUs为共生真菌,隶属于36属,相对丰度25.46%;根围土壤真菌1 513个OTUs中有285个OTUs为共生真菌,隶属于40属,相对丰度59.91%;根内与根围土壤共同拥有共生真菌33属,根内特有3属,根围土壤特有7属。其中,外生菌根真菌为根内和根围土壤中共生真菌的主要类群,分别占共生真菌的98.82%和99.80%。定殖根内的细菌共获得5 550个OTUs,隶属于400属;根围土壤细菌获得8 406个OTUs,隶属于436属,根内细菌群落的Shannon指数和Chao1指数均低于根围土壤的。PICRUSt功能预测分析结果表明,根内的信号转导通路与信号分子和相互作用通路（包括CAM配体、ECM-受体相互作用等通路）的丰度低于根围土壤,而膜运输通路与信号分子和相互作用通路（包括细菌毒素、细胞抗原等通路）的丰度高于根围土壤。根内与根围土壤中菌根辅助细菌组成差异分析结果表明,除慢生根瘤菌属 Bradyrhizobium外,根内其余9属的相对丰度均高于根围土壤,尤其假单胞菌属 Pseudomonas的相对丰度远高于根围土壤。