Isolation and characterization of a motile hydrogenotrophic methanogen from rice paddy field soil in Japan

A hydrogenotrophic motile methanogen was isolated from flooded Japanese paddy field soil. Anaerobic incubation of the paddy soil on H(2)-CO(2) at 20 degrees C led to the enrichment of symmetrically curved motile autofluorescent rods. The methanogenic strain TM20-1 isolated from the culture was halotolerant and utilized H(2)-CO(2), 2-propanol-CO(2), or formate as a sole methanogenic substrate. Based on the 16S rRNA gene sequence similarity (94.8%) with Methanospirillum hungateii, and on the physiological and phenotypic characteristics, TM20-1 was suggested to be a newly identified species belonging to the genus Methanospirillum. This is the first report of isolation of the genus Methanospirillum strain from a rice paddy field.     

Mineralisation of plant nitrogen following alternate wet and dry conditions

Summary Methods designed to measure the cation-exchange properties of plant tissues have been reviewed. They depend on the replacement of the exchangeable cations of the tissues by H⁺, which is then determined directly, or indirectly by exchange for another cation, usually calcium.A rapid and reproducible method using dried milled plant material has been developed which employs acid-washing followed by titration to pH 7 using a glass electrode. This method has been used successfully for measuring the cation-exchange capacity (C.E.C.) of different tissues of a wide range of higher and lower plants, and gives values which correlate well with their related uronic acid content.     

Adaptation of ammonia-oxidizing microorganisms to environment shift of paddy field soil

Adaptation of microorganisms to the environment is a central theme in microbial ecology. The objective of this study was to investigate the response of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) to a soil medium shift. We employed two rice field soils collected from Beijing and Hangzhou, China. These soils contained distinct AOB communities dominated by Nitrosomonas in Beijing rice soil and Nitrosospira in Hangzhou rice soil. Three mixtures were generated by mixing equal quantities of Beijing soil and Hangzhou soil (BH), Beijing soil with sterilized Hangzhou soil (BSH), and Hangzhou soil with sterilized Beijing soil (HSB). Pure and mixed soils were permanently flooded, and the surface-layer soil where ammonia oxidation occurred was collected to determine the response of AOB and AOA to the soil medium shift. AOB populations increased during the incubation, and the rates were initially faster in Beijing soil than in Hangzhou soil. Nitrosospira (cluster 3a) and Nitrosomonas (communis cluster) increased with time in correspondence with ammonia oxidation in the Hangzhou and Beijing soils, respectively. The 'BH' mixture exhibited a shift from Nitrosomonas at day 0 to Nitrosospira at days 21 and 60 when ammonia oxidation became most active. In 'HSB' and 'BSH' mixtures, Nitrosospira showed greater stimulation than Nitrosomonas, both with and without N amendment. These results suggest that Nitrosospira spp. were better adapted to soil environment shifts than Nitrosomonas. Analysis of the AOA community revealed that the composition of AOA community was not responsive to the soil environment shifts or to nitrogen amendment.     

Transformation of soil and fertilizer nitrogen in paddy soil and their availability to rice plants

Summary A pot experiment in the field showed that addition of ammonium sulfate increased the uptake of soil nitrogen. A-value was found to be independent of the rate of nitrogen application. The rice plant took up about 13 percent of the nitrogen in rice straw which was incorporated into the soil when nitrogen fertilizer was not added, and about 15 percent when 50 ppm N was added. Addition of different levels of fertilizer did not affect the release of immobilized fertilizer nitrogen. Recovery of fertilizer by the rice plant was low when nitrogen was added as basal (broadcast). Recovery was improved by incorporating fertilizer nitrogen before transplanting. Recovery of fertilizer nitrogen when topdressed at reproductive stages was much higher than when applied as basal. A fairly large portion of fertilizer nitrogen was immobilized into the soil. Availability of immobilized nitrogen in the soil appeared low. re]19751117     

Characteristics of an anaerobic, syntrophic, butyrate-degrading bacterium in paddy field soil

The number of syntrophic butyrate-degrading bacteria in a flooded paddy field soil was 1.7 x 10(3) MPN/g dry soil. Butyrate was degraded to acetate and methane when paddy soils were incubated anaerobically with the addition of butyrate. However, butyrate degradation was completely suppressed by the addition of the specific inhibitor of methanogenesis, 2-bromoethanesulfonate (BES) to the soil. A hydrogen-using methanogen, strain TM-8, was isolated from flooded paddy field soil. Strain TM-8 was identified as Methanobacterium formicicum based on its physiology and phylogeny. Syntrophic butyrate-degrading bacteria were enumerated and isolated using strain TM-8. A syntrophic butyrate-degrading bacterium, strain TB-6, was isolated in coculture with strain TM-8 from paddy soil. The strain was Gram-negative, had curved rods, and grew on crotonate. Sulfate was not used as an electron acceptor. Strain TB-6 was closely related to S. wolfei subsp. wolfei. The relation between strain TB-6 and the members of Syntrophomonas are discussed.     

Responses of Antarctic soil microbial communities and associated functions to temperature and freeze-thaw cycle frequency

Climatic changes will not only result in higher overall temperature, but also in greater variability in weather conditions. Antarctic soils are subjected to extremely variable conditions in the form of frequent freeze–thaw cycles (FTCs), but the importance of alteration in FTC frequency, compared with increases in average temperature and indirect vegetation-mediated effects on soil microorganisms, is still unknown. We therefore designed two complementary microcosm experiments using undisturbed soil cores from Signy Island (60°43'S, 45°38'W) in the maritime Antarctic. The experiments consisted of soil core incubations with or without the overlying vegetation at four different temperatures and six different FTC regimes. We assessed bacterial and fungal density and community structure, as well as the density of several key genes in microbial nutrient cycles using a combination of RNA- and DNA-based molecular fingerprinting and quantitative PCR approaches in addition to enzymatic activity assays. Results showed that bacteria were more affected by warming than by changes in FTC frequency. In contrast, fungal community structure and abundance were mostly influenced by FTC frequency, as well as the presence of vegetation cover. The relative densities of several bacterial gene families involved in key steps of the N-cycle were affected by FTCs, while warming had little or no effect. The FTCs and incubation temperature also strongly influenced laccase enzymatic activity in soil. In total, our results suggest that, in addition to climatic warming, increased climatic variability may also have a profound impact on Antarctic microbial communities. Although these effects are difficult to detect with assays of total bacterial community structure, they do become manifest in the analysis of key functional gene densities.     

Methanogenic symbionts of anaerobic ciliates and their contribution to methanogenesis in an anoxic rice field soil

Methanogenesis in rice field soils starts soon after flooding while potentially competing processes like reduction of sulphate and iron take place. Early methanogenesis is mainly driven by hydrogen, while later in the season acetate tends to become more important. Anaerobic ciliates are abundant during this period, and their endosymbionts use hydrogen produced by the ciliates to reduce carbon dioxide to methane. These endosymbiotic methanogens are protected from the competition for substrates with other bacteria that may control methanogenesis outside the protozoan cells. Thus, we focussed on early methanogenesis and on the potential contribution from ciliates and their endosymbionts. Only ciliates of the genus Metopus were found to harbour methanogens, as identified by the F(420)-fluorescence of the endosymbionts. We followed the population dynamics of the ciliates with time, and calculated the ratio of symbiotic methane production to overall methanogenesis. Symbiotic methane production was calculated from the species-specific numbers of methanogenic endosymbionts times the cell-specific methane production of the symbionts. According to this calculation, the symbionts' contribution to overall methane production was only 6.4% at the beginning and decreased with time. In a second experiment, colchicine and cycloheximide were used to inhibit all eukaryotes, comparing the remaining methane production rate to a control without inhibitors. In the inhibition experiment, the contribution from symbionts decreased from 40% to 6% during the first days after flooding, and dropped to near zero within 2 weeks. However, nearly all methane produced from H(2)/CO(2) could be attributed to the ciliates' symbionts between days 5 and 10 after flooding. Both experiments showed that the contribution of methanogenic symbionts to overall methane production is a transient phenomenon, restricted to the first 2 weeks.     

碳输入方式对森林土壤碳库和碳循环的影响研究进展

凋落物和植物根系是森林土壤有机碳的主要来源.综述了不同碳输入方式对土壤全碳、微生物生物量碳和可溶性有机碳等碳库组分及土壤呼吸影响的研究进展.不同地区、不同森林土壤有机碳对碳输入的响应程度不同,且采用添加和去除凋落物,以及去除根系方法(DIRT)对土壤碳的影响具有树种差异和区域差异.目前主要侧重于土壤呼吸和碳库组分的研究,亟需开展对土壤碳的结构类型和稳定性,以及土壤生物尤其是土壤动物的响应机制的相关研究.     

Long-term field fertilization alters the diversity of autotrophic bacteria based on the ribulose-1,5-biphosphate carboxylase/oxygenase (RubisCO) large-subunit genes in paddy soil

Carbon dioxide (CO₂) assimilation by autotrophic bacteria is an important process in the soil carbon cycle with major environmental implications. The long-term impact of fertilizer on CO₂ assimilation in the bacterial community of paddy soils remains poorly understood. To narrow this knowledge gap, the composition and abundance of CO₂-assimilating bacteria were investigated using terminal restriction fragment length polymorphism and quantitative PCR of the cbbL gene [that encodes ribulose-1,5-biphosphate carboxylase/oxygenase (RubisCO)] in paddy soils. Soils from three stations in subtropical China were used. Each station is part of a long-term fertilization experiment with three treatments: no fertilizer (CK), chemical fertilizers (NPK), and NPK combined with rice straw (NPKM). At all of the stations, the cbbL-containing bacterial communities were dominated by facultative autotrophic bacteria such as Rhodopseudomonas palustris, Bradyrhizobium japonicum, and Ralstonia eutropha. The community composition in the fertilized soil (NPK and NPKM) was distinct from that in unfertilized soil (CK). The bacterial cbbL abundance (3–8?×?10⁸ copies g soil^?1) and RubisCO activity (0.40–1.76 nmol CO₂ g soil^?1 min^?1) in paddy soils were significantly positively correlated, and both increased with the addition of fertilizer. Among the measured soil parameters, soil organic carbon and pH were the most significant factors influencing the community composition, abundance, and activity of the cbbL-containing bacteria. These results suggest that long-term fertilization has a strong impact on the activity and community of cbbL-containing bacterial populations in paddy soils, especially when straw is combined with chemical fertilizers.     

Life cycle greenhouse gas emissions of palm oil production by wet and dry extraction processes in Thailand

Purpose

The crude palm oil (CPO) extraction is normally done by a wet extraction process, and wastewater treatment of the wet process emits high levels of greenhouse gases (GHGs). A dry process extracts mixed palm oil (MPO) from palm fruit without using water and has no GHG emissions from wastewater treatment. This work is aimed at determining the GHG emissions of a dry process and at evaluating GHG savings on changing from wet to dry process, including land use change (LUC) effects.

Methods

Life cycle assessment from cradle to gate was used. The raw material is palm fruits. The dry process includes primary production, oil room, and utilities. MPO is the main product, while palm cake and fine palm residue are co-products sold for animal feed. Case studies were undertaken without and with carbon stocks of firewood and of nitrogen recycling at plantations from fronds. Allocations by mass, economic, and heating values were conducted. The trading of GHG emissions from co-products to GHG emissions from animal feed was assessed. The GHG emissions or savings from direct LUC (dLUC) and from indirect LUC (iLUC) effects and for the change from wet to dry process were determined.

Results and discussion

Palm fruit and firewood were the major GHG emission sources. Nitrogen recycling on plantations from fronds significantly affects the GHG emissions. With the carbon stocks, the GHG emissions allocated by energy value were 550 kg CO₂ eq/t MPO. The GHG emissions were affected by ?3 to 37% for the change from wet to dry process. When the plantation area was increased by 1 ha and the palm oil extraction was changed from wet to dry process, and the change included dLUC and iLUC, the GHG savings ranged from ?0.94 to 5.08 t CO₂ eq/ha year. The iLUC was the main GHG emission source. The GHG saving mostly originated from the change of extraction process and from the dLUC effect. Based on the potential use of biodiesel production from oil palm, during 2015–2036 in Thailand, when the extraction process was changed and dLUC and iLUC effects were included, the saving in GHG emissions was estimated to range from ?35,454 to 274,774 t CO₂ eq/year.

Conclusions

The change of palm oil extraction process and the LUC effects could minimize the GHG emissions from the palm oil industry. This advantage encourages developing policies that support the dry extraction process and contribute to sustainable developments in palm oil production.

     

免耕与秸秆高留茬还田对抛秧稻田土壤酶活性的影响

利用大田试验,研究了免耕+秸秆还田、免耕、常耕+秸秆还田、常耕4种耕作方式对稻田土壤剖面不同层次土壤酶活性的影响.结果表明:4种耕作方式的酶活性在土壤剖面上表现为上层高于下层,其中免耕+秸秆处理上、下土层间的差异大于其他处理.上层土壤的脲酶、酸性磷酸酶、蛋白酶和纤维素酶活性为免耕处理大干常耕处理,有秸秆还田处理大干无秸秆还田处理,以免耕+秸秆处理最高,常耕处理最低;下层土壤4种酶活性以常耕+秸秆处理最高,免耕+秸秆处理次之,免耕和常耕处理较低.水稻不同生育时期,脲酶和纤维素酶活性在分蘖期较低,增加至孕穗期达到峰值,至成熟时又降至低值;酸性磷酸酶活性以分蘖期较高,拔节期较低;蛋白酶活性在分蘖期和抽穗期分别出现峰值.     

El Niño and dry season rainfall influence hostplant phenology and an annual butterfly migration from Neotropical wet to dry forests

We censused butterflies flying across the Panama Canal at Barro Colorado Island (BCI) for 16 years and butterfly hostplants for 8 years to address the question: What environmental factors influence the timing and magnitude of migrating Aphrissa statira butterflies? The peak migration date was earlier when the wet season began earlier and when soil moisture content in the dry season preceding the migration was higher. The peak migration date was also positively associated with peak leaf flushing of one hostplant (Callichlamys latifolia) but not another (Xylophragma seemannianum). The quantity of migrants was correlated with the El Niño Southern Oscillation, which influenced April soil moisture on BCI and total rainfall in the dry season. Both hostplant species responded to El Niño with greater leaf flushing, and the number of adults deriving from or laying eggs on those new leaves was greatest during El Niño years. The year 1993 was exceptional in that the number of butterflies migrating was lower than predicted by the El Niño event, yet the dry season was unusually wet for an El Niño year as well. Thus, dry season rainfall appears to be a primary driver of larval food production and population outbreaks for A. statira. Understanding how global climate cycles and local weather influence tropical insect migrations improves the predictability of ecological effects of climate change.     

热带森林群落土壤种子库对海拔梯度的响应

在西双版纳海拔800~1400 m的热带森林中,设置海拔梯度垂直样带和样地,研究热带森林群落土壤种子库对海拔梯度的响应。结果发现:(1)土壤种子库的密度和物种丰富度在海拔800 m最大,分别为10540±1578粒·m-2和71个种,最小的土壤种子库密度和物种丰富度则分别出现在海拔1400 m和1200 m。基于Bray-Curtis相似性系数,对4个海拔的土壤种子库物种进行了NMDS排序,发现不同海拔土壤种子库物种组成存在显著的空间分异。(2)土壤种子库中的异质性成分丰富度也因海拔不同存在差异,海拔800 m有9个异质性成分种,海拔1400 m只有5个;而异质性成分种的多度却在海拔1200 m最大。(3)土壤种子库与地上植被的相似性在4个海拔带都低于15%。研究表明,海拔变化对土壤种子库的密度、物种组成格局都能产生显著影响。     

Enrichment of anaerobic nitrate-dependent methanotrophic ‘ Candidatus Methanoperedens nitroreducens’ archaea from an Italian paddy field soil

Paddy fields are a significant source of methane and contribute up to 20% of total methane emissions from wetland ecosystems. These inundated, anoxic soils featuring abundant nitrogen compounds and methane are an ideal niche for nitrate-dependent anaerobic methanotrophs. After 2 years of enrichment with a continuous supply of methane and nitrate as the sole electron donor and acceptor, a stable enrichment dominated by ‘Candidatus Methanoperedens nitroreducens’ archaea and ‘Candidatus Methylomirabilis oxyfera’ NC10 phylum bacteria was achieved. In this community, the methanotrophic archaea supplied the NC10 phylum bacteria with the necessary nitrite through nitrate reduction coupled to methane oxidation. The results of qPCR quantification of 16S ribosomal RNA (rRNA) gene copies, analysis of metagenomic 16S rRNA reads, and fluorescence in situ hybridization (FISH) correlated well and showed that after 2 years, ‘Candidatus Methanoperedens nitroreducens’ had the highest abundance of (2.2 ± 0.4 × 108) 16S rRNA copies per milliliter and constituted approximately 22% of the total microbial community. Phylogenetic analysis showed that the 16S rRNA genes of the dominant microorganisms clustered with previously described ‘Candidatus Methanoperedens nitroreducens ANME2D’ (96% identity) and ‘Candidatus Methylomirabilis oxyfera’ (99% identity) strains. The pooled metagenomic sequences resulted in a high-quality draft genome assembly of ‘Candidatus Methanoperedens nitroreducens Vercelli’ that contained all key functional genes for the reverse methanogenesis pathway and nitrate reduction. The diagnostic mcrA gene was 96% similar to ‘Candidatus Methanoperedens nitroreducens ANME2D’ (WP_048089615.1) at the protein level. The ‘Candidatus Methylomirabilis oxyfera’ draft genome contained the marker genes pmoCAB, mdh, and nirS and putative NO dismutase genes. Whole-reactor anaerobic activity measurements with methane and nitrate revealed an average methane oxidation rate of 0.012 mmol/h/L, with cell-specific methane oxidation rates up to 0.57 fmol/cell/day for ‘Candidatus Methanoperedens nitroreducens’. In summary, this study describes the first enrichment and draft genome of methanotrophic archaea from paddy field soil, where these organisms can contribute significantly to the mitigation of methane emissions.     

Sensitivity of methanogenic bacteria from paddy soil to oxygen and desiccation

Abstract The effects of combinations of desiccation and exposure to O₂ were studied in pure cultures of Methanosarcina barkeri strain Fusaro and in a new Methanosarcina strain and a new Methanobacterium strain which were both isolated from dry oxic paddy soil. Incubation of bacterial suspensions under air for 200 min resulted in a decreased potential to produce CH₄, but not in a decreased viability. The inhibitory effect of O₂ slightly increased with increased salt concentration. Desiccation of bacterial suspensions under N₂ resulted in reduction of viability to 10% and of potential CH₄ production to 0.6%. Desiccation of bacterial suspensions under air resulted in a larger decrease of both viability (0.5%) and potential CH₄ production (0.03%). This decrease was smaller at rapid compared to slow desiccation. Survival and potential CH₄ production were further inhibited when the suspension was dried in the presence of sand grains or glass beads coated with FeS or FeNH₄PO₄. However, survival and potential CH₄ production increased dramatically in the presence of pyrite (FeS₂) grains. Then, as much as 10% of the initial methanogenic population survived oxic desiccation. This relatively good resistance is in agreement with observations that methanogens in rice fields survive the periods when the paddy soil is dry and oxic.     

Responses of soil biota and nitrogen availability to an invasive plant under aboveground herbivory

Plant and Soil - Recently, much attention has been paid to the plant-mediated effects of aboveground herbivory on soil ecosystems. However, studies about the herbivore-induced effects of invasive...