Anoxic Soil Research Articles

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. NH 4 +-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.

Influence of Rhizosphere Oxygen Concentration on Rice Root Growth

The growth of rice root needs oxygen, which is consumed in root respiration and contained in soil also influencing the ecological environment of rhizosphere. Although rice plant can transport atmospheric oxygen from its shoot through its continu-ous aerenchymatous system to its roots, rice can not grow well in submerged, anoxic soil; there exists affinitive relation between the aeration condition of soil and the growth of rice plant. In this study, various rice cultivars were cultivated in hydropotic to study the influence of rhizosphere oxygen concentration enhanced by aeration on rice root growth. The results showed that aera-tion significantly increased the oxygen concentration of hydroponic solution during the whole plant growth stage. Rice plant had the highest oxygen absorption ability at heading stage, compared to the no rice planting treatment, the oxygen concentration at this stage was decreased 73.62% for Guodao 1 and 68.50% for Shanyou 63, and the decrease extent was more than that at booting stage and grain filling stage. Compared to control, length of single root, length of the longest root of rice planted in higher oxygen concentration solution were longer, the dry weight percent of rice root ranging from 10 to 20 cm and longer than 20 cm from root base to tip increased accordingly, and the number of roots per plant was less. While in the treatment with anoxic condition, the number of rice root increased and the length decreased. Genotype difference existed in the influence of rhizosphere oxygen con-centration on root vitality. Under aeration condition, the root active absorption area per plant and root vitality of hybrid rice Guo-dao 1 and Shanyou 63 increased significantly at full heading stage; the root vitality of conventional rice genotype Xiangzaoxian 11 and Yongjing 18 which had high root vitality also increased significantly, while the root vitality changed little in low root vital-ity genotype Xiangzaoxian 24 and Chunjiang 06. When rice growed in anoxic condition, root vitality decreased.

Subsidence Reversal in a Re-Established Wetland in the Sacramento-San Joaquin Delta, California, USA

The stability of levees in the Sacramento-San Joaquin Delta is threatened by continued subsidence of Delta peat islands. Up to 6 meters of land-surface elevation has been lost in the 150 years since Delta marshes were leveed and drained, primarily from oxidation of peat soils. Flooding subsided peat islands halts peat oxidation by creating anoxic soils, but net accumulation of new material in restored wetlands is required to recover land-surface elevations. We investigated the subsidence reversal potential of two 3 hectare, permanently flooded, impounded wetlands re-established on a deeply subsided field on Twitchell Island. The shallower wetland (design water depth 25 cm) was almost completely colonized by dense emergent marsh vegetation within two years; whereas, the deeper wetland (design water depth 55 cm) which developed spatially variable depths as a result of heterogeneous colonization by emergent vegetation, still had some areas remaining as open water after nine years. Changes in land-surface elevation were quantified using repeated sedimentation-erosion table measurements. New material accumulating in the wetlands was sampled by coring. Land-surface elevations increased by an average of 4 cm/yr in both wetlands from 1997 to 2006; however, the rates at different sites in the wetlands ranged from -0.5 to +9.2 cm/yr. Open water areas of the deeper wetland without emergent vegetation had the lowest rates of land-surface elevation gain. The greatest rates occurred in areas of the deeper wetland most isolated from the river water inlets, with dense stands of emergent marsh vegetation (tules and cattails). Vegetated areas of the deeper wetland in the transition zones between open water and mature emergent stands had intermediate rates of land-surface gain, as did the entire shallower wetland. These results suggest that the dominant component contributing to land-surface elevation gain in these wetlands was accumulation of organic matter, rather than mineral sediment, and that accumulation of organic matter in emergent marshes is strongly affected by hydrologic factors. Re-established, non-tidal wetlands with managed hydrology can produce significant increases in land-surface elevations, which can help to improve levee stability and protect subsided islands from future flooding.

Development of a Genetic System for the Denitrifying Bacterium ‘Aromatoleum aromaticum’ Strain EbN1

Members of the betaproteobacterial ‘Aromatoleum’/Azoarcus/Thauera cluster contribute to the biodegradation of aromatic and other recalcitrant compounds in anoxic soils and sediments. The metabolically versatile ‘Aromatoleumaromaticum’ strain EbN1 represents a model organism for this cluster, having already been studied on the physiological, proteogenomic and biochemical level. Here we report the development of a genetic system for ‘A. aromaticum’ strain EbN1 enabling unmarked deletion mutagenesis by heterologous recombination and subsequent complementation. The antibiotic sensitivity of strain EbN1 was characterized and optimal conditions for efficient cultivation on solid medium were established. A procedure for introducing foreign DNA into strain EbN1 by conjugation was developed. The effectiveness of the genetic system was demonstrated by unmarked in-frame deletion of ebdC2, encoding the γ-subunit of a paralogous ethylbenzene dehydrogenase.

Characterization of redox-related soil microbial communities along a river floodplain continuum by fatty acid methyl ester (FAME) and 16S rRNA genes

Redox states affect substrate availability and energy transformation, and, thus, play a crucial role in regulating soil microbial abundance, diversity, and community structure. We evaluated microbial communities in soils under oxic, intermittent, and anoxic conditions along a river floodplain continuum using fatty acid methyl ester (FAME) and 16S rRNA genes-based terminal-restriction fragment length polymorphism (T-RFLP) bacterial fingerprints. In all the soils tested, microbial communities clustered according to soil redox state by both evaluation techniques. Bacteria were dominant components of soil microbial communities, while mycorrhizal fungi composed about 12% of the microbial community in the oxic soils. Gram-positive bacteria consisted >10% of the community in all soils tested and their abundance increased with increasing soil depth when shifting from oxic to anoxic conditions. In the anoxic soils, Gram-positive bacteria composed about 16% of the total community, suggesting that their growth and maintenance were not as sensitive to oxygen supply as for other microbes. In general, microorganisms were more abundant and diverse, and distributed more evenly in the oxic layers than the anoxic layers. The decrease in abundance with increasing oxygen and substrate limitation, however, was considerably more drastic than the decrease in diversity, suggesting that growth of soil microorganisms is more energy demanding than maintenance. The lower diversity in the anoxic than the oxic soils was attributed primarily to the differences in oxygen availability in these soils.

Multisecular corrosion behaviour of low carbon steel in anoxic soils: Characterisation of corrosion system on archaeological artefacts

In the context of the prediction of materials behaviour used in the nuclear waste storage, the understanding of iron corrosion mechanisms in anoxic environment is of great importance. Information can be obtained using complementary analytical tools. Interactions between burial soil and archaeological artefacts are studied by performing on site soil measurements. Moreover, archaeological artefacts are studied on transverse sections using a combination of microbeam techniques. The specific interest of this project lies in the study of ferrous thick corrosion layers formed in anoxic environments.

Comparing the mutagenicity of toxaphene after aging in anoxic soils and accumulating in fish

A test program was conducted to evaluate the mutagenicity of toxaphene residuals extracted from aged soils and from fish collected in creeks near a toxaphene-contaminated site. The ultimate objective was to determine if the residual toxaphene congeners were more or less mutagenic than those in technical-grade toxaphene. The study showed that the mutagenicity of the bioaccumulated toxaphene congeners in fish, expressed as colony revertants per μg of residual toxaphene, was no greater than that of technical-grade toxaphene. The mutagenic impact of the toxaphene residuals in aged soil statistically was less than that for technical-grade toxaphene. Two specific congeners, a hexachlorobornane (labeled Hx-Sd) and a heptachlorobornane (labeled Hp-Sd), were found to accumulate over time in both soil and fish extracts, but did not show increased mutagenic impacts relative to that produced by technical-grade toxaphene.

Dynamics of the Methanogenic Archaeal Community during Plant Residue Decomposition in an Anoxic Rice Field Soil

Incorporation of plant residues strongly enhances the methane production and emission from flooded rice fields. Temperature and residue type are important factors that regulate residue decomposition and CH(4) production. However, the response of the methanogenic archaeal community to these factors in rice field soil is not well understood. In the present experiment, the structure of the archaeal community was determined during the decomposition of rice root and straw residues in anoxic rice field soil incubated at three temperatures (15 degrees C, 30 degrees C, and 45 degrees C). More CH(4) was produced in the straw treatment than root treatment. Increasing the temperature from 15 degrees C to 45 degrees C enhanced CH(4) production. Terminal restriction fragment length polymorphism analyses in combination with cloning and sequencing of 16S rRNA genes showed that Methanosarcinaceae developed early in the incubations, whereas Methanosaetaceae became more abundant in the later stages. Methanosarcinaceae and Methanosaetaceae seemed to be better adapted at 15 degrees C and 30 degrees C, respectively, while the thermophilic Methanobacteriales and rice cluster I methanogens were significantly enhanced at 45 degrees C. Straw residues promoted the growth of Methanosarcinaceae, whereas the root residues favored Methanosaetaceae. In conclusion, our study revealed a highly dynamic structure of the methanogenic archaeal community during plant residue decomposition. The in situ concentration of acetate (and possibly of H(2)) seems to be the key factor that regulates the shift of methanogenic community.

Physiology, Ecology, Phylogeny, and Genomics of Microorganisms Capable of Syntrophic Metabolism

Syntrophic metabolism is diverse in two respects: phylogenetically with microorganisms capable of syntrophic metabolism found in the Deltaproteobacteria and in the low G+C gram-positive bacteria, and metabolically given the wide variety of compounds that can be syntrophically metabolized. The latter includes saturated fatty acids, unsaturated fatty acids, alcohols, and hydrocarbons. Besides residing in freshwater and marine anoxic sediments and soils, microbes capable of syntrophic metabolism also have been observed in more extreme habitats, including acidic soils, alkaline soils, thermal springs, and permanently cold soils, demonstrating that syntrophy is a widely distributed metabolic process in nature. Recent ecological and physiological studies show that syntrophy plays a far larger role in carbon cycling than was previously thought. The availability of the first complete genome sequences for four model microorganisms capable of syntrophic metabolism provides the genetic framework to begin dissecting the biochemistry of the marginal energy economies and interspecies interactions that are characteristic of the syntrophic lifestyle.

Iron-Mediated Microbial Oxidation and Abiotic Reduction of Organic Contaminants under Anoxic Conditions

In anoxic environments, the oxidation of organic compounds, such as BTEX fuel components, by dissimilatory Fe(III) reduction can generate reactive mineral-bound Fe(II) species, which in turn are able to reduce other classes of organic and inorganic groundwater contaminants. In this study, we designed and evaluated an anaerobic batch reactor that mimicks iron-reducing conditions to investigate the factors that favor the coupling of microbial toluene oxidation and abiotic reduction of nitroaromatic contaminants. We investigated the influence of different Fe(III)-bearing minerals and combinations thereof on the coupling of these two processes. Results from laboratory model systems show that complete oxidation of toluene to CO2 by Geobacter metallireducens in the presence of Fe(III)-bearing minerals leads to the formation of mineral-bound Fe(II) species capable of the reduction of 4-nitroacetophenone. Whereas significant microbial toluene oxidation was only observed in the presence of amorphous Fe(III) phases, reduction of nitroaromatic compounds only proceeded with Fe(II) species bound to crystalline Fe(III) oxides. Our results suggest that in anoxic soils and sediments containing amorphous and crystalline iron phases simultaneously, coupling of microbial oxidation and abiotic reduction of organic compounds may allow for concurrent natural attenuation of different contaminant classes.

Quantification of carbon flow from stable isotope fractionation in rice field soils with different organic matter content

Rice fields are an important source for the greenhouse gas methane produced by acetoclastic and hydrogenotrophic methanogenesis. Fractionation of 13C/ 12C can in principle be used to quantify the relative contribution of these pathways, but our knowledge of isotopic fractionation during reduction of CO 2 and turnover of acetate in different methanogenic environments is still scarce. We therefore measured δ 13C signatures in two types of anoxic Italian rice field soils, one with high and one with low degradable organic matter (OM) content. Both soils were incubated in the presence and absence of methyl fluoride, a specific inhibitor of acetoclastic methanogenesis. Optimization of methyl fluoride concentration resulted in complete inhibition of acetoclastic methanogenesis. CH 4 was then exclusively produced by hydrogenotrophic methanogenesis, allowing determination of the isotopic signatures and fractionation factors specific for this methanogenic pathway. Acetate, which was then no longer consumed, accumulated and was used for determination of the isotopic signature of the fermentatively produced acetate (both total acetate and methyl carbon of acetate). Hence, all isotopic signatures, including fractionation factors were determined for the methanogenic soil. These data, were then used for computation of the relative contribution of the two methanogenic pathways. In the high OM soil, the contribution of acetoclastic methanogenesis to total CH 4 production increased simultaneously with decreasing acetate concentration. In the low OM soil, methanogenesis from H 2/CO 2 was clearly greater than theoretically expected. Furthermore, isotope fractionation of hydrogenotrophic methanogenesis indicated that the in situ energy status of methanogens strongly depended on the availability of organic carbon in the rice field soil system. Collectively, our data show that the study of isotopic fractionation in methanogenic environments allows a deeper insight into the ongoing processes, which may be quite different in the same ecosystem with different content of degradable OM.

Improved simulation of poorly drained forests using Biome-BGC

Forested wetlands and peatlands are important in boreal and terrestrial biogeochemical cycling, but most general-purpose forest process models are designed and parameterized for upland systems. We describe changes made to Biome-BGC, an ecophysiological process model, that improve its ability to simulate poorly drained forests. Model changes allowed for: (1) lateral water inflow from a surrounding watershed, and variable surface and subsurface drainage; (2) adverse effects of anoxic soil on decomposition and nutrient mineralization; (3) closure of leaf stomata in flooded soils; and (4) growth of nonvascular plants (i.e., bryophytes). Bryophytes were treated as ectohydric broadleaf evergreen plants with zero stomatal conductance, whose cuticular conductance to CO(2) was dependent on plant water content. Individual model changes were parameterized with published data, and ecosystem-level model performance was assessed by comparing simulated output to field data from the northern BOREAS site in Manitoba, Canada. The simulation of the poorly drained forest model exhibited reduced decomposition and vascular plant growth (-90%) compared with that of the well-drained forest model; the integrated bryophyte photosynthetic response accorded well with published data. Simulated net primary production, biomass and soil carbon accumulation broadly agreed with field measurements, although simulated net primary production was higher than observed data in well-drained stands. Simulated net primary production in the poorly drained forest was most sensitive to oxygen restriction on soil processes, and secondarily to stomatal closure in flooded conditions. The modified Biome-BGC remains unable to simulate true wetlands that are subject to prolonged flooding, because it does not track organic soil formation, water table changes, soil redox potential or anaerobic processes.

Biological control potential and modes of action of Bacillus megaterium against Meloidogyne graminicola on rice

This paper describes the development of a biological control system for Meloidogyne graminicola using rice root inoculations of the bacterium, Bacillus megaterium, which was isolated from a rice-growing region of Taiwan. Treatment with B. megaterium resulted in a greater than 40% reduction in nematode penetration and gall formation compared with non-treated rice roots, and, in a separate study, colonization of rice roots with B. megaterium decreased migration of M. graminicola to the root zone by nearly 60% compared with that of non-treated roots. Exposure of M. graminicola eggs to secondary metabolites of B. megaterium reduced hatching by over 60% compared with eggs not exposed to the bacteria. This paper will present modes of action through which B. megaterium reduces M. graminicola damage, and it will discuss challenges in developing nematode biological control systems for rice cultivation in intermittently anoxic and oxic soil environments.

Identification of Acetate-Assimilating Microorganisms under Methanogenic Conditions in Anoxic Rice Field Soil by Comparative Stable Isotope Probing of RNA

Acetate is the most abundant intermediate of organic matter degradation in anoxic rice field soil and is converted to CH(4) and/or CO(2). Aceticlastic methanogens are the primary microorganisms dissimilating acetate in the absence of sulfate and reducible ferric iron. In contrast, very little is known about bacteria capable of assimilating acetate under methanogenic conditions. Here, we identified active acetate-assimilating microorganisms by using a combined approach of frequent label application at a low concentration and comparative RNA-stable isotope probing with (13)C-labeled and unlabeled acetate. Rice field soil was incubated anaerobically at 25 degrees C for 12 days, during which (13)C-labeled acetate was added at a concentration of 500 muM every 3 days. (13)C-labeled CH(4) and CO(2) were produced from the beginning of the incubation and accounted for about 60% of the supplied acetate (13)C. RNA was extracted from the cells in each sample taken and separated by isopycnic centrifugation according to molecular weight. Bacterial and archaeal populations in each density fraction were screened by reverse transcription-PCR-mediated terminal restriction fragment polymorphism analysis. No differences in the bacterial populations were observed throughout the density fractions of the unlabeled treatment. However, in the heavy fractions of the (13)C treatment, terminal restriction fragments (T-RFs) of 161 bp and 129 bp in length predominated. These T-RFs were identified by cloning and sequencing of 16S rRNA as from a Geobacter sp. and an Anaeromyxobacter sp., respectively. Apparently these bacteria, which are known as dissimilatory iron reducers, were able to assimilate acetate under methanogenic conditions, i.e., when CO(2) was the predominant electron acceptor. We hypothesize that ferric iron minerals with low bioavailability might have served as electron acceptors for Geobacter spp. and Anaeromyxobacter spp. under these conditions.

Preference of wet dune species for waterlogged conditions can be explained by adaptations and specific recruitment requirements

The preference of wetland angiosperms for waterlogged soils has been explained by several hypotheses: (1) wetland species are adapted to waterlogging and sensitive to drought; (2) wetland species are tolerant to drought, but inferior competitors at drier conditions; (3) wetland species have narrow moisture optima for recruitment. We tested these hypotheses by the application of permanent and fluctuating water levels to experimental wet dune plant communities with four species that frequently occur in wet dune slacks ( Carex flacca, Molinia caerulea, Samolus valerandi and Schoenus nigricans) and one competitive species of drier conditions ( Calamagrostis epigejos). After 3 years, fluctuating water levels had led to lower total biomass production than permanent water levels, indicating that switching from aerated to anoxic soil conditions involved physiological costs. The collective biomass of wetland species was highest at permanently waterlogged conditions with interspecific variation in the biomass optima. At the nutrient-poor growth conditions of this long-term experiment, biomass of Calamagrostis was independent of water level treatment, thus the hypothesized competitive superiority of this species at drier conditions could not explain the biomass responses of the wetland species in this study. Instead, this is evidence for an ecological preference of adult wet dune plants for waterlogged to moist conditions. Recruitment of most wet dune slack species occurred in a narrower range of water levels than adult growth, indicating that recruitment requirements also pose a limitation to the distribution of these wet dune species. Incorporation of recruitment into nature management support models may improve their predictions.

Erratum

European Journal of Soil ScienceVolume 57, Issue 5 p. 755-755 Free Access Erratum This article corrects the following: Dynamics of the methanogenic archaeal community in anoxic rice soil upon addition of straw R. Conrad, M. Klose, Volume 57Issue 4European Journal of Soil Science pages: 476-484 First Published online: March 3, 2006 First published: 05 September 2006 https://doi.org/10.1111/j.1365-2389.2006.00865.xAboutSectionsPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat In Dijkstra et al. (2006) there was an error in Figure 2. The correct figure, as it should have been reproduced, is shown below. Figure 2Open in figure viewerPowerPoint δ 15N (‰) of soil total (soil), extractable (extr) and chloroform-labile (micr) fractions (a),δ15N (‰) of NO3− and NH4+ (b), Δ15NMU (δ15N of chloroform-labile N minusδ15N extractable N) and Δ15NMS (δ15N of chloroform-labile N minusδ15N soil total N, ‰) (c) in relation to distance from the water resevoir (means, n = 3–4, bars indicate ± one standard error). Different letters within a row indicate significant differences between means (DMRT) for that variable. Reference Dijkstra, P., Menyailo, O.V., Doucett, R.R., Hart, S.C., Schwartz, E. & Hungate, B.A. 2006. C and N availability affects the 15N. European Journal of Soil Science, 57, 468– 475. Wiley Online LibraryWeb of Science®Google Scholar Volume57, Issue5October 2006Pages 755-755 FiguresReferencesRelatedInformation

Xylanibacter oryzae gen. nov., sp. nov., a novel strictly anaerobic, Gram-negative, xylanolytic bacterium isolated from rice-plant residue in flooded rice-field soil in Japan

A strictly anaerobic, xylanolytic bacterium, strain KB3(T), isolated from rice-plant residue in flooded anoxic rice-field soil in Japan, was characterized phenotypically and phylogenetically. Cells were Gram-negative, non-motile, non-spore-forming, short to filamentous rods. Growth of the strain was remarkably stimulated by the addition of haemin to the medium. The novel strain utilized various sugars including xylan, xylose, pectin and carboxymethylcellulose and produced acetate, propionate and succinate with a small amount of malate. Propionate production was stimulated by the addition of a B-vitamin mixture or cobalamin to the medium. The novel strain was slightly acidophilic with an optimum pH 5.7-6.2 and the optimum growth temperature was 30 degrees C. Oxidase, catalase and nitrate-reducing activities were negative. Aesculin was hydrolysed. The major cellular fatty acids were anteiso-C(15 : 0) and iso-3-OH C(17 : 0). The major respiratory quinones were menaquinones MK-12(H(2)) and MK-13(H(2)). The genomic DNA G+C content was 43.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequence placed the strain in the phylum Bacteroidetes. The closest related species was Prevotella bivia with a 16S rRNA gene sequence similarity of 89.5 %. Prevotella albensis and Prevotella oulorum were the next closest recognized species with sequence similarities of 89.1 %. Based on a comprehensive examination of the differences in phylogenetic, ecological, physiological and chemotaxonomic characteristics of strain KB3(T) and those of related species, a novel genus and species, Xylanibacter oryzae gen. nov., sp. nov., is proposed to accommodate strain KB3(T). The type strain of the novel species is KB3(T) (=JCM 13648(T)=DSM 17970(T)).

Production and consumption of ethylene in temperate volcanic forest surface soils

SummaryTo date our knowledge is limited with regard to the cycling of ethylene (C2H4) in temperate forest soils containing volcanic ash, and the effect of forest‐to‐orchard conversion on its cycling. We studied ethylene accumulation in such forest soils by oxic and anoxic incubations, along with the stimulatory effect of glucose addition on soil C2H4 accumulation. We also studied the effect of antibiotics and autoclaving on C2H4 production and consumption by volcanic forest soils, and the cycling of C2H4 and CH4 in surface soils after conversion of a Japanese cedar forest to an orchard. Ethylene production and consumption by forest surface soils results from a microbial process, and soil streptomycin‐sensitive bacteria make a minor contribution. Soil C2H4 accumulation was much larger during anoxic than during oxic incubation, which indicates that anoxic conditions can induce C2H4 accumulation in forest soils. Glucose addition as a carbon source can sharply increase C2H4 accumulation rates in the anoxic and oxic forest soils during the first week of incubation. However, there was no difference in total C2H4 accumulation in the amended and non‐treated soils after 35 days of anoxic incubation. Ethylene production of the 0–5 cm and 5–10 cm soils beneath forest and orchard showed the greatest rate after 2 weeks of anoxic incubation when soil CH4 production started to increase sharply, and later it was strongly suppressed. The forest‐to‐orchard conversion showed little influence on the CH4 production of surface soils during short‐term anoxic incubation, but significantly reduced soil C2H4 production. The conversion also significantly decreased the consumption of soil CH4 and C2H4, the former more than the latter. Soil properties such as total C, water‐soluble organic C and pH contribute to the consumption and production of C2H4 in the 0–5 cm and 5–10 cm soils, and there are the parallels between CH4 and C2H4 consumption in soils, which suggests the presence of similar microorganisms. Long‐term anoxic conditions of in situ surface upland soils are normally not prevalent, so it can be reasonably concluded that there is a larger C2H4 accumulation rather than CH4 accumulation in surface soils beneath forest and orchard after heavy rainfall, especially beneath forest.

Redox Fluctuations Frame Microbial Community Impacts on N-cycling Rates in a Humid Tropical Forest Soil

Fluctuating soil redox regimes may facilitate the co-occurrence of microbial nitrogen transformations with significantly different sensitivities to soil oxygen availability. In an upland humid tropical forest, we explored the impact of fluctuating redox regimes on gross nitrogen cycling rates and microbial community composition. Our results suggest that the rapidly fluctuating redox conditions that characterize these upland soils allow anoxic and oxic N processing to co-occur. Gross nitrogen mineralization was insensitive to soil redox fluctuations. In contrast, nitrifiers in this soil were directly affected by low redox periods, yet retained some activity even after 3–6 weeks of anoxia. Dissimilatory nitrate reduction to ammonium (DNRA) was less sensitive to oxygen exposure than expected, indicating that the organisms mediating this reductive process were also tolerant of unfavorable (oxic) conditions. Denitrification was a stronger sink for NO3− in consistently anoxic soils than in variable redox soils. Microbial biomass and community composition were maintained with redox fluctuation, but biomass decreased and composition changed under static oxic and anoxic soil regimes. Bacterial community structure was significantly correlated with rates of nitrification, denitrification and DNRA, suggesting that redox-control of soil microbial community structure was an important determinant of soil N-cycling rates. Specific nitrogen cycling functional groups in this environment (such as nitrifiers, DNRA organisms, and denitrifiers) appear to have adapted to nutrient resources that are spatially and temporally variable. In soils where oxygen is frequently depleted and re-supplied, characteristics of microbial tolerance and resilience can frame N cycling patterns.

Soil Attributes in a Sierra Nevada Riparian Meadow as Influenced by Grazing

Data on the effects of livestock grazing on soil nutrient availability are virtually nonexistent for meadow systems. We measured the effect of livestock grazing on soil, emphasizing soil-solution chemistry, in a Sierra Nevada riparian meadow. Treatments were livestock exclusion (begun in 1989) and grazing to leave 1 000 kg � ha � 1 of vegetation. Ceramic tension lysimeters were placed in the treatments (2 replicates) by landscape position (stream edge, midfloodplain, and forest edge), and by depth (approximately 0.1, 0.6, and 1.2 m below the soil surface). Lysimeter water was extracted twice monthly in April, May, and June of 1990 through 1993, and cations and anions were quantified. In addition, KCl-extractable NO3 � and NH4 þ ; bicarbonate-extractable ortho-P; available Mn, Cu, Fe, and Zn; and root-length density (RLD) were quantified in soils by treatment, landscape position, and soil depth in July 1991 and September 1993. RLD was not affected by grazing. Significant (P � 0.05) treatment effects were largely limited to the forest edge. The grazed treatment had greater lysimeter-extractable Na þ , Ca þ2 ,M g þ2 , and NO3 � ; higher pH; and less K þ and NH4 þ than the excluded treatment. Compared with corresponding excluded treatments, bicarbonate-extractable P was significantly greater on the grazed forest edge, and available Mn was significantly greater at the grazed stream-edge position in 1991. Extractable NO3 � was significantly higher in the 0‐25 cm depth increment of the grazed treatment, and available Zn was significantly greater on the grazed midfloodplain position in 1993. Grazing did not result in more anoxic soil conditions than the excluded treatment. Grazing effects were most pronounced at the forest edge, possibly as a result of spatial transfer of nutrients via cow urine and feces. Management goals to sustain highelevation meadows should emphasize maintenance of high RLD to sequester soil nutrients.