scholarly journals Cyanate is a low abundance but actively cycled nitrogen compound in soil

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Maria Mooshammer ◽  
Wolfgang Wanek ◽  
Stephen H. Jones ◽  
Andreas Richter ◽  
Michael Wagner
Keyword(s):  
Energy Source ◽  
Management Practices ◽  
Nitrogen Compound ◽  
Terrestrial Ecosystems ◽  
Rice Paddy ◽  
Ammonia Oxidizers ◽  
Rice Paddy Soil ◽  
Isotope Tracer ◽  
Tracer Experiments

AbstractCyanate can serve as a nitrogen and/or carbon source for different microorganisms and as an energy source for autotrophic ammonia oxidizers. However, the extent of cyanate availability and utilisation in terrestrial ecosystems and its role in biogeochemical cycles is poorly known. Here we analyse cyanate concentrations in soils across a range of soil types, land management practices and climates. Soil cyanate concentrations were three orders of magnitude lower than ammonium or nitrate. We determined cyanate consumption in a grassland and rice paddy soil using stable isotope tracer experiments. We find that cyanate turnover was rapid and dominated by biotic processes. We estimated that in-situ cyanate production rates were similar to those associated with urea fertilizer decomposition, a major source of cyanate in the environment. We provide evidence that cyanate is actively turned over in soils and represents a small but continuous nitrogen/energy source for soil microbes.

scholarly journals Cyanate – a low abundant but actively cycled nitrogen compound in soil

2020 ◽  
Author(s):  
M. Mooshammer ◽  
W. Wanek ◽  
S. H. Jones ◽  
A. Richter ◽  
M. Wagner
Keyword(s):  
Energy Source ◽  
Soil Microbes ◽  
Nitrogen Compound ◽  
Terrestrial Ecosystems ◽  
Selective Advantage ◽  
Environmental Significance ◽  
Available Nitrogen ◽  
Genetic Potential ◽  
Low Concentrations

AbstractCyanate (NCO-) can serve as a nitrogen and/or carbon source for different microorganisms and even additionally as an energy source for autotrophic ammonia oxidizers. Despite the widely distributed genetic potential for direct cyanate utilization among bacteria, archaea and fungi, the availability and environmental significance of cyanate is largely unknown, especially in terrestrial ecosystems. We found relatively low concentrations of soil cyanate, but its turnover was rapid. Contrary to our expectations, cyanate consumption was clearly dominated by biotic processes, and, notably, cyanate was produced in-situ at rates similar to that of cyanate formation from urea fertilizer, which is believed to be one of the major sources of cyanate in the environment. Our study provides evidence that cyanate is actively turned over in soils and represents a small but continuous nitrogen/energy source for soil microbes, potentially contributing to a selective advantage of microorganisms capable of direct cyanate utilization.One-sentence summaryCyanate represents a small but continuously available nitrogen source for soil microbes, contributing to a selective advantage of microorganisms capable of direct cyanate utilization.

scholarly journals Rice paddyNitrospiraeencode and express genes related to sulfate respiration: proposal of the new genusCandidatusSulfobium

2017 ◽  
Author(s):  
Sarah Zecchin ◽  
Ralf C. Mueller ◽  
Jana Seifert ◽  
Ulrich Stingl ◽  
Karthik Anantharaman ◽  
...  
Keyword(s):  
Sulfate Reduction ◽  
Paddy Soil ◽  
Rice Paddy ◽  
Bulk Soil ◽  
Sulfur Cycling ◽  
Dissimilatory Sulfate Reduction ◽  
Rice Paddy Soil ◽  
Novel Genus ◽  
Environmental Surveys

AbstractNitrospiraespp. distantly related to thermophilic, sulfate-reducingThermodesulfovibriospecies are regularly observed in environmental surveys of anoxic marine and freshwater habitats. However, little is known about their genetic make-up and physiology. Here, we present the draft genome ofNitrospiraebacterium Nbg-4 as a representative of this clade and analyzed itsin situprotein expression under sulfate-enriched and sulfate-depleted conditions in rice paddy soil. The genome of Nbg-4 was assembled from replicated metagenomes of rice paddy soil that was used to grow rice plants in the presence and absence of gypsum (CaSO4×2H2O). Nbg-4 encoded the full pathway of dissimilatory sulfate reduction and showed expression thereof in gypsum-amended anoxic bulk soil as revealed by parallel metaproteomics. In addition, Nbg-4 encoded the full pathway of dissimilatory nitrate reduction to ammonia, which was expressed in bulk soil without gypsum amendment. The relative abundance of Nbg-4-related metagenome reads was similar under both treatments indicating that it maintained stable populations while shifting its energy metabolism. Further genome reconstruction revealed the potential to utilize butyrate, formate, H2, or acetate as electron donor, with the Wood-Ljungdahl pathway being expressed under both conditions. Comparison to publicly availableNitrospiraegenome bins confirmed that the pathway for dissimilatory sulfate reduction is also present in relatedNitrospiraerecovered from groundwater. Subsequent phylogenomics showed that such microorganisms form a novel genus within the phylumNitrospirae, with Nbg-4 as a representative species. Based on the widespread occurrence of this novel genus, we propose for Nbg-4 the nameCandidatusSulfobium mesophilum, gen. nov., spec. nov.ImportanceRice paddies are indispensable for food supply but are a major source of the greenhouse gas methane. If not counterbalanced by cryptic sulfur cycling, methane emission from rice paddy fields would be even higher. However, the microorganisms involved in this sulfur cycling are little understood. By using an environmental systems biology approach of Italian rice paddy soil, we could retrieve the population genome of a novel member of the phylumNitrospirae. This microorganism encoded the full pathway of dissimilatory sulfate reduction and expressed itin situunder sulfate-enriched and anoxic conditions. Phylogenomics and comparison to environmental surveys showed that such microorganisms are actually widespread in freshwater and marine environments. At the same time, they represent a yet undiscovered genus within the little exploredNitrospirae. Our results will be important to design enrichment strategies and postgenomic studies to fully understand the contribution of these novelNitrospiraeto the global sulfur cycle.

Niche differentiation of ammonia oxidizers and nitrite oxidizers in rice paddy soil

2013 ◽  
Vol 15 (8) ◽  
pp. 2275-2292 ◽  
Author(s):  
Xiubin Ke ◽  
Roey Angel ◽  
Yahai Lu ◽  
Ralf Conrad
Keyword(s):  
Paddy Soil ◽  
Niche Differentiation ◽  
Rice Paddy ◽  
Ammonia Oxidizers ◽  
Rice Paddy Soil ◽  
Nitrite Oxidizers

scholarly journals Research in Vegetation House on the Possible Use of Microorganisms in Bioremediation of Soils Contaminated with Crude Oil

2011 ◽  
Vol 68 (1) ◽  
Author(s):  
Lavinia PARVAN ◽  
Delia CARABIS ◽  
M. TOTI
Keyword(s):  
Energy Source ◽  
Soil Fertility ◽  
Crude Oil ◽  
Physiological Activity ◽  
Terrestrial Ecosystems ◽  
Oil Hydrocarbons ◽  
The World ◽  
Bacterial Inoculum

Within the remediation methods experimented all over the world, the bioremediation in situ based on the activity of microorganisms to use the oil hydrocarbons as carbon and energy source, is considered the most effective, especially, because it does not involves the severe and irreversible disruption of structure and, implicitly, the pedogenic characteristics of affected soil and its cost is relatively low. The microorganisms represent probably the most important component of terrestrial ecosystems, which by their highly diverse physiological activity are the basis of the functions creating soil fertility. The N100P100K100 fertilization treatment and application of bacterial inoculum proved the most effective so far.

scholarly journals Phylogenetic Diversity, Localization, and Cell Morphologies of Members of the Candidate Phylum TG3 and a Subphylum in the Phylum Fibrobacteres, Recently Discovered Bacterial Groups Dominant in Termite Guts

2006 ◽  
Vol 72 (10) ◽  
pp. 6780-6788 ◽  
Author(s):  
Yuichi Hongoh ◽  
Pinsurang Deevong ◽  
Satoshi Hattori ◽  
Tetsushi Inoue ◽  
Satoko Noda ◽  
...  
Keyword(s):  
Geographic Distance ◽  
Rice Paddy ◽  
Specific Detection ◽  
Rice Paddy Soil ◽  
Specific Primers ◽  
Host Genus ◽  
Gut Symbionts ◽  
Group 3 ◽  
Bacterial Groups

ABSTRACT Recently we discovered two novel, deeply branching lineages in the domain Bacteria from termite guts by PCR-based analyses of 16S rRNA (Y. Hongoh, P. Deevong, T. Inoue, S. Moriya, S. Trakulnaleamsai, M. Ohkuma, C. Vongkaluang, N. Noparatnaraporn, and T. Kudo, Appl. Environ. Microbiol. 71:6590-6599, 2005). Here, we report on the specific detection of these bacteria, the candidate phylum TG3 (Termite Group 3) and a subphylum in the phylum Fibrobacteres, by fluorescence in situ hybridization in the guts of the wood-feeding termites Microcerotermes sp. and Nasutitermes takasagoensis. Both bacterial groups were detected almost exclusively from the luminal fluid of the dilated portion in the hindgut. Each accounted for approximately 10% of the total prokaryotic cells, constituting the second-most dominant groups in the whole-gut microbiota. The detected cells of both groups were in undulate or vibroid forms and apparently resembled small spirochetes. The cell sizes were 0.2 to 0.4 by 1.3 to 6.0 μm and 0.2 to 0.3 by 1.3 to 4.9 μm in the TG3 and Fibrobacteres, respectively. Using PCR screenings with specific primers, we found that both groups are distributed among various termites. The obtained clones formed monophyletic clusters that were delineated by the host genus rather than by the geographic distance, implying a robust association between these bacteria and host termites. TG3 clones were also obtained from a cockroach gut, lake sediment, rice paddy soil, and deep-sea sediments. Our results suggest that the TG3 and Fibrobacteres bacteria are autochthonous gut symbionts of various termites and that the TG3 members are also widely distributed among various other environments.

Road Salt Application in Highland Creek Watershed, Toronto, Ontario - Chloride Mass Balance

2010 ◽  
Vol 45 (4) ◽  
pp. 451-461 ◽  
Author(s):  
Nandana Perera ◽  
Bahram Gharabaghi ◽  
Peter Noehammer ◽  
Bruce Kilgour
Keyword(s):  
Mass Balance ◽  
Management Practices ◽  
Chloride Concentration ◽  
Aquatic Organisms ◽  
Terrestrial Ecosystems ◽  
Road Salt ◽  
Winter Period ◽  
Chloride Mass Balance ◽  
Creek Watershed ◽  
Chloride Concentrations

Abstract Occurrence of increasing chloride concentrations in urban streams of cold climates, mainly due to road salt application, has raised concerns on its adverse effects on aquatic and terrestrial ecosystems. Therefore, there is a need for a better understanding of processes associated with road salt application and subsequent discharge into the environment in order to develop management practices to minimize detrimental effects of chlorides. The chloride mass analysis for the Highland Creek watershed based on four years of hourly monitoring data indicates that approximately 60% of the chlorides applied on the watershed enter streams prior to subsequent salting period, 85% of which occurs during the period between November and March. Contribution of private de-icing operations on chloride mass input within Highland Creek watershed was estimated to be approximately 38%, indicating its significance in overall chloride mass balance. Salt application rates, as well as chloride output in the streams, vary spatially based on land use, influencing chloride concentrations in surface waters. The estimated groundwater chloride concentration of 275 mg/L indicates that some aquatic organisms in Highland Creek would potentially be at risk even outside the winter period under dry weather flow conditions.

Soil seed bank and vegetation dynamics in Sahelian fallows; the impact of past cropping and current grazing treatments

2004 ◽  
Vol 20 (6) ◽  
pp. 683-691 ◽  
Author(s):  
Bruno Hérault ◽  
Pierre Hiernaux
Keyword(s):  
Seed Bank ◽  
Management Practices ◽  
Soil Seed Bank ◽  
Residual Effects ◽  
Ex Situ ◽  
Phosphorus Fertilizer ◽  
Wet Season ◽  
Seed Extraction ◽  
The Impact

The soil seed bank in a 5-y-old Sahelian fallow was studied through seed extraction and compared with germinations recorded either in controlled conditions, ex situ in a glasshouse, or in the field. The influence of phosphorus fertilizer and mulch application during the preceding crop period, and that of seasonal grazing regimes applied the last 2 y of fallowing, were assessed on the composition of the seed stock. Ctenium elegans, Fimbristylis hispidula, Merremia pinnata and Phyllanthus pentandrus accounted together for 75% of extracted seeds, 72% of ex situ, and 62% of in situ seedlings. Mulch treatment was correlated with the first axis of the canonical correspondence analyses performed on the seedling datasets. Mulch and phosphorus fertilizer treatments held similar responses, as they both favoured the seed bank of erect dicotyledons such as P. pentandrus and Cassia mimosoides. On the whole, the effects of grazing remained modest compared with the residual effects of past crop management practices. However, seedling densities increased as a result of dry-season grazing, while the soil seed bank decreased with wet-season grazing. Grazing also reduced the spatial heterogeneity of the seed bank rather than the overall number of species.

Water-washed hydrochar in rice paddy soil reduces N2O and CH4 emissions: A whole growth period investigation

2021 ◽  
Vol 274 ◽  
pp. 116573
Author(s):  
Danyan Chen ◽  
Yibo Zhou ◽  
Cong Xu ◽  
Xinyu Lu ◽  
Yang Liu ◽  
...  
Keyword(s):  
Paddy Soil ◽  
Growth Period ◽  
Rice Paddy ◽  
Rice Paddy Soil ◽  
Ch4 Emissions

scholarly journals Mercury methylation in paddy soil: source and distribution of mercury species at a Hg mining area, Guizhou Province, China

2016 ◽  
Vol 13 (8) ◽  
pp. 2429-2440 ◽  
Author(s):  
Lei Zhao ◽  
Christopher W. N Anderson ◽  
Guangle Qiu ◽  
Bo Meng ◽  
Dingyong Wang ◽  
...  
Keyword(s):  
Paddy Soil ◽  
Surface Soil ◽  
Ambient Air ◽  
Rice Paddy ◽  
Guizhou Province ◽  
Mercury Species ◽  
Low Concentration ◽  
Paddy Water ◽  
Hg Mining

Abstract. Rice paddy plantation is the dominant agricultural land use throughout Asia. Rice paddy fields have been identified as important sites for methylmercury (MeHg) production in the terrestrial ecosystem and a primary pathway of MeHg exposure to humans in mercury (Hg) mining areas. We compared the source and distribution of Hg species in different compartments of the rice paddy during a complete rice-growing season at two different typical Hg-contaminated mining sites in Guizhou province, China: an abandoned site with a high Hg concentration in soil but a low concentration in the atmosphere and a current-day artisanal site with a low concentration in soil but a high concentration in the atmosphere. Our results showed that the flux of new Hg to the ecosystem from irrigation and atmospheric deposition was insignificant relative to the pool of old Hg in soil; the dominant source of MeHg to paddy soil is in situ methylation of inorganic Hg (IHg). Elevated MeHg concentrations and the high proportion of Hg as MeHg in paddy water and the surface soil layer at the artisanal site demonstrated active Hg methylation at this site only. We propose that the in situ production of MeHg in paddy water and surface soil is dependent on elevated Hg in the atmosphere and the consequential deposition of new Hg into a low-pH anoxic geochemical system. The absence of depth-dependent variability in the MeHg concentration in soil cores collected from the abandoned Hg mining site, consistent with the low concentration of Hg in the atmosphere and high pH of the paddy water and irrigation water, suggested that net production of MeHg at this site was limited. We propose that the concentration of Hg in ambient air is an indicator for the risk of MeHg accumulation in paddy rice.

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