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 α, β, and γ 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.     

Characterization of Microbial Consortia in Paddy Rice Soil by Phospholipid Analysis

Abstract Microbial biomass and community structure in paddy rice soil during the vegetation period of rice were estimated by analysis of their phospholipid fatty acids (PLFA), hydroxy fatty acids of lipopolysaccharides (LPS-HYFA), and phospholipid ether lipids (PLEL) directly extracted from the soil. A clear change in the composition of the community structure at different sampling periods was observed, indicated by the principal component analysis of the PLFA. A dramatic decline of ester-linked PLFA was observed in the soil samples taken at the second sampling time. In contrast to the ester-linked PLFA, the non-ester-linked PLFA composition did not change. The hydroxy fatty acids of lipopolysaccharides as well as ether lipids decreased consecutively during the observation period. Total microbial abundance was estimated to be (4.1–7.3) × 10⁹ cells g^-1 soil (dry weight). About 44% account for aerobic and 32% for facultative anaerobic bacteria, and 24% for archaea, on average. According to the profile and patterns of PLFA in the soil sample, it may be suggested that the paddy soil at the August sampling period contained more abundant facultative anaerobic bacteria (ca. 36%) and archaea (ca. 37%), but the total microbial biomass was significantly lower than in the remaining sampling periods. As the plant approached maturity, the microbial community structure in the soil changed to contain more abundant Gram-negative bacteria and methanotrophs. Received: 23 September 1999; Accepted: 28 February 2000; Online Publication: 12 May 2000     

Depth-Dependent Differences in Community Structure of the Human Colonic Microbiota in Health

Objective

The aims of this study were to develop techniques for spatial microbial assessment in humans and to establish colonic luminal and mucosal spatial ecology, encompassing longitudinal and cross-sectional axes.

Design

A microbiological protected specimen brush was used in conjunction with a biopsy forceps to sample the colon in nine healthy volunteers undergoing colonoscopy. Terminal Restriction Fragment Length Polymorphism analysis was used to determine the major variables in the spatial organization of the colonic microbiota.

Results

Protected Specimen Brush sampling retrieved region-specific, uncontaminated samples that were enriched for bacterial DNA and depleted in human DNA when compared to biopsy samples. Terminal Restriction Fragment Length Polymorphism analysis revealed a segmentation of bacterial communities between the luminal brush and biopsy-associated ecological niches with little variability across the longitudinal axis of the colon and reduced diversity in brush samples.

Conclusion

These results support the concept of a microbiota with little longitudinal variability but with some degree of segregation between luminal and mucosal communities.     

Forces and Straw Cutting Performance of Double Disc Furrow Opener in No-Till Paddy Soil

Conservation tillage is an energy efficient and low cost tillage system to improve soil environment compared with conventional tillage systems. However, the rice residue management becomes an “impossible to achieve” task due to high soil moisture content at harvest time and the thickness of rice straw. Disc type furrow openers are used for both seed drilling as well as straw cutting during no tillage sowing. A study was conducted to evaluate the draft requirement and straw cutting performances of different sized furrow openers in no-till paddy soil conditions. Double disc furrow opener was tested on an in-field traction bench for three working depths, i.e. 30, 60 and 90 mm, and three forwarding speeds, i.e. 0.1, 0.2 and 0.3 m/s. The draft and vertical forces on the disc were recorded with load cells. These sensors were connected to a data acquisition system developed with hardware and software. The results revealed that the size of the furrow opener, operating depth and the forwarding speed had significant effects (P<0.05) on the horizontal and vertical forces, and the straw cutting performance. Mean values of the draft were 648.9, 737.2 and 784.6 N for the opener with diameters of 330, 450 and 600 mm respectively, and the vertical forces for similar openers were 904.7, 1553.9 and 1620.4 N, respectively. Furthermore, the mean straw cutting efficiencies for the double disc opener with diameters of 330, 450 and 600 mm were 39.36, 78.47 and 65.46%, respectively. The opener with 450 mm diameter provided higher straw cutting efficiency as compared to 600 mm diameter disc, while lowest straw cutting efficiency was observed with 330 mm diameter disc. The 450 mm diameter opener provided the highest straw cutting efficiency (88.6%) at 90 mm working depth and expressed optimum performance compared with other furrow openers.     

Diversity and Structure of the Methanogenic Community in Anoxic Rice Paddy Soil Microcosms as Examined by Cultivation and Direct 16S rRNA Gene Sequence Retrieval

A dual approach consisting of cultivation and molecular retrieval of partial archaeal 16S rRNA genes was carried out to characterize the diversity and structure of the methanogenic community inhabiting the anoxic bulk soil of flooded rice microcosms. The molecular approach identified four groups of known methanogens. Three environmental sequences clustered with Methanobacterium bryantii and Methanobacterium formicicum, six were closely related but not identical to those of strains of Methanosaeta concilii, two grouped with members of the genus Methanosarcina, and two were related to the methanogenic endosymbiont of Plagiopyla nasuta. The cultivation approach via most-probable-number counts with a subsample of the same soil as an inoculum yielded cell numbers of up to 10⁷ per g of dry soil for the H₂-CO₂-utilizing methanogens and of up to 10⁶ for the acetate-utilizing methanogens. Strain VeH52, isolated from the terminal positive dilution on H₂-CO₂, grouped within the phylogenetic radiation characterized by M. bryantii and M. formicicum and the environmental sequences of the Methanobacterium-like group. A consortium of two distinct methanogens grew in the terminal positive culture on acetate. These two organisms showed absolute 16S rRNA gene identities with environmental sequences of the novel Methanosaeta-like group and the Methanobacterium-like group. Methanosarcina spp. were identified only in the less-dilute levels of the same dilution series on acetate. These data correlate well with acetate concentrations of about 11 μM in the pore water of this rice paddy soil. These concentrations are too low for the growth of known Methanosarcina spp. but are at the acetate utilization threshold of Methanosaeta spp. Thus, our data indicated Methanosaeta spp. and Methanobacterium spp. to be the dominant methanogenic groups in the anoxic rice soil, whereas Methanosarcina spp. appeared to be less abundant.     

Differences of Soil Microbial Biomass and Nitrogen Transformation under Two Forest Types in Central Germany

In order to observe the tree species effect on soil N status, soil microbial biomass C and N (C_mic, N_mic), potential N mineralization and potential nitrification (under laboratory incubation conditions, 22 °C) in different subhorizons (LOf₁, Of₂, Oh and mineral soil at 0–10 cm depth) were determined at three forest sites in central Germany. At each site, two contrasting stands (Beech, Norway spruce or Scots pine) were selected, where the initial soil conditions were similar. Three sampling dates that represented different stages of tree growth were selected: growing season - August, dormant season - November, after budbreak – April. In organic layers, C_mic-to-total C (C_t) ratios under beech and under conifer were 0.72–4.74% and 0.34–2.11%, respectively. N_mic-to-total N (N_t) ratios were 2.47–11.61% and 0.71–5.77%, respectively. Both concentrations of C_mic and N_mic were significantly affected by the stand type and sampling time. Potential N mineralization rates, ranging from 3.7 to 19.7 mg N kg⁻¹ d⁻¹, showed no clear pattern in relation to stand type. However, potential nitrification rates were mostly significantly higher under beech than under contrasting conifer. In mineral soils, concentrations of C_mic and N_mic showed a clear temporal pattern in the order: August>November>April. The average N_mic and N_mic-to-N_t were higher in soils from beech than conifer, while C_mic and C_mic-to-C_t ratios were similar between the two forest types. In organic layers, the highest values of C_mic-to-N_mic ratio and C_mic were found in November samples, especially under beech. By contrast, in mineral soils the highest value of C_mic-to-N_mic ratios were found in April samples, and at that time the C_mic concentrations were the lowest, especially under conifer. These results revealed the differences in microbial growth form and survival strategy associated with different tree species and soil layers.     

Microbial Populations Responsive to Denitrification-Inducing Conditions in Rice Paddy Soil,as Revealed by Comparative 16S rRNA Gene Analysis

Rice paddy soil has been shown to have strong denitrifying activity. However, the microbial populations responsible for nitrate respiration and denitrification have not been well characterized. In this study, we performed a clone library analysis of >1,000 clones of the nearly full-length 16S rRNA gene to characterize bacterial community structure in rice paddy soil. We also identified potential key players in nitrate respiration and denitrification by comparing the community structures of soils with strong denitrifying activity to those of soils without denitrifying activity. Clone library analysis showed that bacteria belonging to the phylum Firmicutes, including a unique Symbiobacterium clade, dominated the clones obtained in this study. Using the template match method, several operational taxonomic units (OTUs), most belonging to the orders Burkholderiales and Rhodocyclales, were identified as OTUs that were specifically enriched in the sample with strong denitrifying activity. Almost one-half of these OTUs were classified in the genus Herbaspirillum and appeared >10-fold more frequently in the soils with strong denitrifying activity than in the soils without denitrifying activity. Therefore, OTUs related to Herbaspirillum are potential key players in nitrate respiration and denitrification under the conditions used.Rice is one of the most important agronomic plants in the world (20). More than 135 million ha are used for rice cultivation worldwide, 88% of which consists of paddy fields (i.e., flooded fields) (16). Since rice paddy soil has limited available oxygen, various anaerobic biochemical processes can occur, including methane production, Mn⁴⁺ and Fe³⁺ reduction, nitrate respiration, and denitrification.Denitrification is a microbial respiratory process during which soluble nitrogen oxides (NO₃⁻ and NO₂⁻) are reduced to gaseous products (NO, N₂O, and N₂) (14, 43). Reduction of nitrate (NO₃⁻) to nitrite (NO₂⁻) is part of the denitrification process; however, this reaction can also be performed by nondenitrifiers. Reduction of nitrate to nitrite as an end product is called nitrate respiration (43). The emission of N₂O from rice paddy soils is less than that from upland crop fields (2), which is probably due to complete nitrate-nitrite reduction to N₂, since rice paddy soil is known to have strong denitrifying activity (28). However, the microbes responsible for denitrification in rice paddy soil are not well known.Denitrifying ability is sporadically distributed among taxonomically diverse groups of bacteria, as well as some archaea and fungi (14, 33, 43). Therefore, it is difficult to identify denitrifying organisms based only on their 16S rRNA gene sequences (33). However, culture-independent 16S rRNA gene analysis can be used to identify microbial populations responsive to denitrification-inducing conditions if they are properly differentiated from background populations. The 16S rRNA gene can provide taxonomic information about organisms which cannot be obtained from analyses targeting nitrite reductase genes (nirS and nirK) alone (34).One approach to differentiate functionally active populations from background populations is to use stable-isotope probing (SIP) (35). SIP was previously used to identify succinate-assimilating bacterial populations under denitrifying conditions in rice paddy soil, using nitrate and succinate as the electron acceptor and donor, respectively (37). Although SIP analysis can provide solid evidence that links function with taxonomy, it requires assimilation of isotopically labeled substrates. This may limit the application of SIP in studies of dissimilatory processes, such as nitrate respiration and denitrification. For example, previous SIP studies targeted bacteria assimilating ¹³C-labeled acetate, methanol, or succinate under denitrifying conditions (13, 30, 37).Another approach is to detect specifically enriched microbial populations under certain conditions by comparative analysis of 16S rRNA gene sequences (9). This approach does not necessarily require addition of isotopically labeled substrates and therefore has the potential to identify microbes performing dissimilatory processes. Furthermore, the community structure of the total population can also be elucidated in this manner (10, 25, 36). However, the usefulness of comparative analysis of 16S rRNA gene sequences has not been thoroughly tested. In addition, this approach has not been used to study nitrate respirators and denitrifiers.Consequently, the objectives of this study were (i) to characterize the soil bacterial population in rice paddy soil by clone library analysis of >1,000 clones of the nearly full-length 16S rRNA gene and (ii) to identify active bacterial populations under denitrification-inducing conditions by comparing clone libraries.     

Partitioning of CH4 and CO2 Production Originating from Rice Straw,Soil and Root Organic Carbon in Rice Microcosms

Flooded rice fields are an important source of the greenhouse gas CH₄. Possible carbon sources for CH₄ and CO₂ production in rice fields are soil organic matter (SOM), root organic carbon (ROC) and rice straw (RS), but partitioning of the flux between the different carbon sources is difficult. We conducted greenhouse experiments using soil microcosms planted with rice. The soil was amended with and without ¹³C-labeled RS, using two ¹³C-labeled RS treatments with equal RS (5 g kg⁻¹ soil) but different δ¹³C of RS. This procedure allowed to determine the carbon flux from each of the three sources (SOM, ROC, RS) by determining the δ¹³C of CH₄ and CO₂ in the different incubations and from the δ¹³C of RS. Partitioning of carbon flux indicated that the contribution of ROC to CH₄ production was 41% at tillering stage, increased with rice growth and was about 60% from the booting stage onwards. The contribution of ROC to CO₂ was 43% at tillering stage, increased to around 70% at booting stage and stayed relatively constant afterwards. The contribution of RS was determined to be in a range of 12–24% for CH₄ production and 11–31% for CO₂ production; while the contribution of SOM was calculated to be 23–35% for CH₄ production and 13–26% for CO₂ production. The results indicate that ROC was the major source of CH₄ though RS application greatly enhanced production and emission of CH₄ in rice field soil. Our results also suggest that data of CH₄ dissolved in rice field could be used as a proxy for the produced CH₄ after tillering stage.     

Influence of Temperature and Oil Content on the Soil/Air Partition Coefficient for Hexachlorobenzene in Oil-Contaminated Rice Paddy Field Soil

The soil/air partition coefficients (K _SA ) for hexachlorobenzene (HCB) in oil-contaminated (crude oil and diesel) rice paddy field soils were measured in a solid fugacity meter at different oil concentrations over the temperature range of 5 to 30°C at 100% relative humidity. The results showed that values of K _SA increased with a decrease of temperature. As for oil content, there is a critical separate phase concentration (CSPC) above which K _SA increased with increasing of oil content. When oil content is above CSPC, oil plays a role as a separate phase that enhances the sorption capacity of the soil. At a given temperature (20°C) values of CSPC depended on the natural organic matter (NOM) contents of the soil, while for a given oil concentration they depended on the temperature. The normalized oil/air partition coefficients ) for HCB deduced from K _SA for oils and experimentally determined with crude oil/quartz sand system were similar and 0.7–7 times higher than the normalized organic/air partition coefficient ), which implied that oil was a super sorbent. The enthalpies (ΔH_SA) for crude oil and diesel were 64.9 and 55.7 kJ mol^?1, respectively.     

Basal and Foliar Treatment using an Organic Fertilizer Amendment Lowers Cadmium Availability in Soil and Cadmium Uptake by Rice on Field Micro-Plot Experiment Planted in Contaminated Acidic Paddy Soil

In the present study, field micro-plot experiments were conducted to investigate the basal and foliar application of a tested organic fertilizer amendment (OFA) for decreasing the risk of Cd accumulating in rice. The results showed that applications of OFA significantly increased rice yields in Cd-polluted soil and reduced the level of Cd in rice plants, especially in rice grain. In addition, three application methods of OFA were investigated (single basal application (B1, B2, and B3), combined basal application (+LM, +D, and +Z), and foliar application (F1, F2)). Treat B, F, +LM, +D were all higher than control on rice yield with 25.03, 28.05, 30.61, 22.50 g pot^?1 on average, respectively. Among which, rice cadmium depress to 0.33 mg kg^?1 in foliar application is considered to be a more efficient and economical method of heavy metal remediation. The mechanism of foliar application to alleviate the accumulation of Cd in brown rice may be related to the probable Cd sequestration in the leaves and straws. And the doses of the foliar application were 2.25–3.75 kg hm^?2, approximately 1.0–2.5% of the basal application amount yet with more effect (0.10 mg kg^?1 more than single basal; 0.23 mg kg^?1 more than combined basal) on Cd reduction.     

不同稻作制对红壤性水稻土中锰剖面分布的影响

为了探讨红壤性水稻土锰的迁移和转化行为,通过长达16a的定位试验研究了不同稻作制、有机肥以及地下水位对土壤剖面中全锰、活性锰和交换态锰分布的影响。试验结果表明,长期淹水种稻引起0-20cm土壤层次全锰、活性锰和交换态锰含量的显著下降,而在20－40cm和40－75cm土层相对累积。不同稻作制比较,0－20cm土层中全锰、活性锰和交换态锰含量以稻稻泡显著高于稻稻绿和稻稻油处理,而20－40cm和40－75cm土层3种锰形态的含量各稻作制之间无显著差异,表明实行水旱轮作的稻稻绿与稻稻油两种稻作制耕层土壤锰的淋溶损失比持续淹水的稻稻泡制更为严重。相对而言,不同有机肥施用水平和地下水位对土壤剖面中锰分布的影响要小于稻作制,总的趋势为：土壤剖面中锰的空间分异程度以高量有机肥＞常量有机肥＞单施化肥;低水位＞高水位。从土壤中锰的空间分布规律可以看出,水旱轮作（尤其是在低水位和有机无机配合的条件下）比长期淹水更有利于土壤锰氧化还原引起的深层淋溶与淀积,加速了典型水稻土剖面的形成。     

崇明岛稻田三种种植方式下中小型土壤动物群落多样性

平陆运河是西部陆海新通道的一项重要工程,茅尾海是平陆运河的重要支撑节点。本次调查潮间带大型底栖动物群落,在评估茅尾海生态环境质量的同时,又积累本海域大型底栖动物基线数据,为平陆运河建设期、运营期的科学管理提供科学数据支撑。于2020年10月和2021年1月、4月、7月,在钦州茅尾海东部岸线设置4个采样断面,分别是仙岛公园、沙环村、滨海公园和康王庙村,按照《海洋调查规范》(GB 12763.6-2007)的要求对潮间带大型底栖动物进行采样调查和物种分类鉴定;分析大型底栖动物群落组成、优势种组成及生物多样性指数。调查研究结果表明,茅尾海潮间带大型底栖动物以节肢动物为主,物种占比超过41%,个体数占比超过87%,优势种(IRI > 1 000)有麦克碟尾虫(Discapseudes mackiei)、台湾泥蟹(Ilyoplax formosensis)、隆背大眼蟹(Macrophthalmus convexus)和四齿大额蟹(Metopograpsus quadridentatus),但优势种在4个断面分布不均,仅麦克碟尾虫出现在各断面;主要种(100 ≤ IRI < 1 000)有27种,其中仅扁平拟闭口蟹(Paracleistostoma depressum)、背毛小头虫(Notodasus sp.)出现在各断面;常见种(10 ≤ IRI < 100)有19种,稀有种(IRI < 10)有8种,它们均分布不均;辛普森多样性指数(D)和香农多样性指数(H?)分别为0.435(0.183 ~ 0.704)和1.506(0.747 ~ 2.256),显著低于2009年相应指标,P值分别为0.004和0.048;Pielou均匀度指数(J)均值为0.475(0.223 ~ 0.696),与2009年的Pielou均匀度指数(J)没有显著差异(P = 0.109)。综合丰度-生物量曲线(ABC曲线)、香农多样性指数(H?)、大型底栖动物污染指数(IMP)推断茅尾海目前整体海域生态环境处于中等污染水平。综合上述指标,认为目前茅尾海海域整体生态环境已属于中等程度污染。本次调查建立的茅尾海潮间带大型底栖动物数据库,将为未来平陆运河的生态建设和科学运营提供支撑。     

Propionate Formation by Opitutus terrae in Pure Culture and in Mixed Culture with a Hydrogenotrophic Methanogen and Implications for Carbon Fluxes in Anoxic Rice Paddy Soil

Propionate-forming bacteria seem to be abundant in anoxic rice paddy soil, but biogeochemical investigations show that propionate is not a correspondingly important intermediate in carbon flux in this system. Mixed cultures of Opitutus terrae strain PB90-1, a representative propionate-producing bacterium from rice paddy soil, and the hydrogenotrophic Methanospirillum hungatei strain SK maintained hydrogen partial pressures similar to those in the soil. The associated shift away from propionate formation observed in these cultures helps to reconcile the disparity between microbiological and biogeochemical studies.     

Varietal Differences in the Kinetics of Iron Uptake by Excised Rice Roots

Iron uptake by excised rice roots can be described in kineticterms of active absorption and the formation of ion-carriercomplexes. Conventional interpretation indicates two carriers,one of which is responsible for iron absorption at low concentrations,with the second primarily functioning at high iron levels. Themaximum absorption of both carriers vanes greatly between varieties,the variety Pebifun having much greater absorptive capacitythan either Siam-29 or Paldal. Varietal differences in uptakecapacity primarily depend on total carrier concentration, 0.93,0.40,and 0.31 µ moles per g roots of Pebifun, Siam-29, andPaldal respectively. Although the kinetic treatment suggeststwo carriers, the chromatographic evidence indicates the presenceof the iron primarily in one major initial complex, with suggestionsof accumulation rather than turnover. An alternative to thecarrier hypothesis is therefore put forward which regards theaccumulation of iron as binding initially on to one or severalclosely related substances, followed by incorporation into secondaryproducts when a critical level of the initial product is exceeded.Manganese was found to competitively inhibit iron uptake byrice roots. Inhibition was more severe in Siam-29 than in Paldaland can be explained on the basis of carrier concentration andcompetition for the same carrier site. Copper was found notto be competitive for the iron absorption sites. The effectof copper was not significant with the low levels of iron butonly with the 5 x 10^–4 M Fe level. The effect varied betweenvarieties, in Pebifun both 5 x 10^–5 and 5 x 10^–6M Cu inhibited iron uptake compared with the control. In thecase of Siam-29 both copper levels accelerated iron uptake,5 x 10^–5 M Cu giving the greatest uptake. With 5 x 10^–5M Cu Pebifun took up much less iron than Siam-29. The mecharosmof copper inhibition/stimulation is highly speculative.