The influence of western hemlock and western redcedar on microbial numbers,nitrogen mineralization,and nitrification

Summary Microbial numbers in the forest floor and mineral soil (Al horizon) under large individual western hemlock (Tsuga heterophylla) and western redcedar (Thuja plicata) trees were compared. The lower pH and base saturation of hemlock samples was associated with higher fungal spore counts while cedar samples had higher total microbial counts and populations of ammonium oxidizing bacteria. Nitrogen mineralization rates were greater in laboratory incubations of hemlock soil but nitrification was only observed in incubations of cedar soil. These differences in nitrogen mineralization and nitrification are aspects of species-specific nutrient cycling regimes.     

The influence of mineral fertilizer combined with a nitrification inhibitor on microbial populations and activities in calcareous Uzbekistanian soil under cotton cultivation

Application of fertilizers combined with nitrification inhibitors affects soil microbial biomass and activity. The objective of this research was to determine the effects of fertilizer application combined with the nitrification inhibitor potassium oxalate (PO) on soil microbial population and activities in nitrogen-poor soil under cotton cultivation in Uzbekistan. Fertilizer treatments were N as urea, P as ammophos, and K as potassium chloride. The nitrification inhibitor PO was added to urea and ammophos at the rate of 2%. Three treatments--N200 P140 K60 (T1), N200 PO P140 K60 (T2), and N200 P140 PO K60 (T3) mg kg(-1) soil--were applied for this study. The control (C) was without fertilizer and PO. The populations of oligotrophic bacteria, ammonifying bacteria, nitrifying bacteria, denitrifying bacteria, mineral assimilating bacteria, oligonitrophilic bacteria, and bacteria group Azotobacter were determined by the most probable number method. The treatments T2 and T3 increased the number of oligonitrophilic bacteria and utilization mineral forms of nitrogen on the background of reducing number of ammonifying bacteria. T2 and T3 also decreased the number of nitrifying bacteria, denitrifying bacteria, and net nitrification. In conclusion, our experiments showed that PO combined with mineral fertilizer is one of the most promising compounds for inhibiting nitrification rate, which was reflected in the increased availability and efficiency of fertilizer nitrogen to the cotton plants. PO combined with mineral fertilizer has no negative effects on nitrogen-fixing bacteria Azotobacter and oligo-nitrophilic bacteria.     

Biogeochemical processes in the saline meromictic Lake Kaiike, Japan: implications from molecular isotopic evidences of photosynthetic pigments

Stable carbon and nitrogen isotopic compositions were determined for individual photosynthetic pigments isolated and purified from the saline meromictic Lake Kaiike, Japan, to investigate species-independent biogeochemical processes of photoautotrophs in the natural environment. In the anoxic monimolimnion and benthic microbial mats, the carbon isotopic compositions of BChls e and isorenieratene related to brown-coloured strains of green sulfur bacteria are substantially ( approximately 10 per thousand) depleted in (13)C relative to those found in the chemocline. In conjunction with 16S rDNA evidence reported previously, it strongly suggests that Pelodyctyon luteolum inhabited and photosynthesized in the anoxic monimolimnion and benthic microbial mats by using (13)C-depleted regenerated CO(2). By contrast, both Chl a and BChl a in the monimolimnion and microbial mats have similar isotopic compositions as they do in the chemocline, implying that the source organisms live only in the chemocline. In the chemocline, the nitrogen isotopic compositions of BChl e homologues ranges from -7.7 to-6.5 per thousand, whereas that of BChl a is -2.1 per thousand. These isotopic compositions suggest that green sulfur bacteria Chlorobium phaeovibrioides would conduct nitrogen fixation in the chemocline, whereas purple sulfur bacteria Halochromatium sp. and cyanobacteria Synechococcus sp. may assimilate nitrite.     

Limestone Corrosion by Neutrophilic Sulfur-Oxidizing Bacteria: A Coupled Microbe-Mineral System

Subsurface karst aquifers receiving sulfidic water can host complex chemolithotrophic microbial communities that are capable of dissolving limestone, forming new karstic habitat. Neutrophilic sulfur-oxidizing bacteria use reduced sulfur compounds as energy rich substrate, potentially producing sulfuric acid as a geochemically reactive byproduct. The physicochemical relationship between a biofilm forming on a limestone surface and the extent of microbial influence on dissolution rate, however, are unknown. We investigated the rate of Madison limestone dissolution by sulfur-oxidizers both in the field at Lower Kane Cave, WY (LKC), and in the laboratory using continuous flow culture reactors and microbial mat collected from LKC. In the field, a microbial consortium rapidly colonized limestone chips forming a thick biofilm, with deep etching of mineral surfaces underneath. In the laboratory we found that a microbial biofilm oxidizing thiosulfate on the limestone surface accelerated dissolution rate up to 7 times faster than the abiotic baseline rate. In contrast, experiments done with H₂S or a mixture of H₂S and thiosulfate had no effect on dissolution rate. We hypothesize that the laboratory mat community dominated by Thiothrix sp. oxidizes thiosulfate to sulfate and H⁺, while H₂S is partially oxidized to S°. When all sulfur substrate is withheld, the community oxidizes stored intracellular sulfur, briefly accelerating limestone dissolution even in the absence of external supplied substrate. Accelerated corrosion occurs only in the reactive micro-environment under the biofilm, disconnected from the bulk reactor solution. When experiments are repeated where the microbial population is separated from the limestone by a dialysis membrane barrier, measured pH drop is greater, but there is only slight enhancement of rate. This work confirms our working hypothesis that neutrophilic sulfur-oxidizers colonize and rapidly dissolve limestone surfaces, possibly to buffer the production of excess acidity.     

Effect of dissolved organic carbon quality on microbial decomposition and nitrification rates in stream sediments

1. Microbial decomposition of dissolved organic carbon (DOC) contributes to overall stream metabolism and can influence many processes in the nitrogen cycle, including nitrification. Little is known, however, about the relative decomposition rates of different DOC sources and their subsequent effect on nitrification. 2. In this study, labile fraction and overall microbial decomposition of DOC were measured for leaf leachates from 18 temperate forest tree species. Between 61 and 82% (mean, 75%) of the DOC was metabolized in 24 days. Significant differences among leachates were found for labile fraction rates (P < 0.0001) but not for overall rates (P=0.088). 3. Nitrification rates in stream sediments were determined after addition of 10 mg C L^–1 of each leachate. Nitrification rates ranged from below detection to 0.49 μg N mL sediment^–1 day^–1 and were significantly correlated with two independent measures of leachate DOC quality, overall microbial decomposition rate (r=–0.594, P=0.0093) and specific ultraviolet absorbance (r=0.469, P=0.0497). Both correlations suggest that nitrification rates were lower in the presence of higher quality carbon. 4. Nitrification rates in sediments also were measured after additions of four leachates and glucose at three carbon concentrations (10, 30, and 50 mg C L^–1). For all carbon sources, nitrification rates decreased as carbon concentration increased. Glucose and white pine leachate most strongly depressed nitrification. Glucose likely increased the metabolism of heterotrophic bacteria, which then out‐competed nitrifying bacteria for NH₄⁺. White pine leachate probably increased heterotrophic metabolism and directly inhibited nitrification by allelopathy.     

Dominance of bacterial ammonium oxidizers and fungal denitrifiers in the complex nitrogen cycle pathways related to nitrous oxide emission

Organic compounds and mineral nitrogen (N) usually increase nitrous oxide (N₂O) emissions. Vinasse, a by‐product of bio‐ethanol production that is rich in carbon, nitrogen, and potassium, is recycled in sugarcane fields as a bio‐fertilizer. Vinasse can contribute significantly to N₂O emissions when applied with N in sugarcane plantations, a common practice. However, the biological processes involved in N₂O emissions under this management practice are unknown. This study investigated the roles of nitrification and denitrification in N₂O emissions from straw‐covered soils amended with different vinasses (CV: concentrated and V: nonconcentrated) before or at the same time as mineral fertilizers at different time points of the sugarcane cycle in two seasons. N₂O emissions were evaluated for 90 days, the period that occurs most of the N₂O emission from fertilizers; the microbial genes encoding enzymes involved in N₂O production (archaeal and bacterial amoA, fungal and bacterial nirK, and bacterial nirS and nosZ), total bacteria, and total fungi were quantified by real‐time PCR. The application of CV and V in conjunction with mineral N resulted in higher N₂O emissions than the application of N fertilizer alone. The strategy of vinasse application 30 days before mineral N reduced N₂O emissions by 65% for CV, but not for V. Independent of rainy or dry season, the microbial processes were nitrification by ammonia‐oxidizing bacteria (AOB) and archaea and denitrification by bacteria and fungi. The contributions of each process differed and depended on soil moisture, soil pH, and N sources. We concluded that amoA‐AOB was the most important gene related to N₂O emissions, which indicates that nitrification by AOB is the main microbial‐driven process linked to N₂O emissions in tropical soil. Interestingly, fungal nirK was also significantly correlated with N₂O emissions, suggesting that denitrification by fungi contributes to N₂O emission in soils receiving straw and vinasse application.     

Transformations of ammonia and the environmental impact of nitrifying bacteria

In the sequence of events leading from ammonia to N₂ during the process of biotransformation of inorganic nitrogen compounds, the weakest link, with respect to our knowledge and understanding of the organisms involved, is nitrification. In particular, this is true for the oxidation of ammonia to nitrite. The enzymes have not been thoroughly studied, and the enzymatic mechanisms have not been identified. Almost any biochemical and physiological aspect studied proved to be controversial, and major ecological questions still remain unanswered. Unless the structure and function of the various components of the process are worked out, progress in developing means for controlling nitrification will depend mainly on laborious trial and error and not on knowledgeable manipulation of this group of bacteria.Abbreviations AMO ammonia monooxygenase - HAO hydroxylamine oxidoreductase - MPN most probable number - TCE trichloroethylene     

Molecular analysis of the diversity of nitrifying bacteria in the soils of the forest and steppe zones of European Russia

Nitrifying bacteria play a key role in the global nitrogen cycle due to their ability to convert reduced nitrogen compounds (ammonium) to oxidized ones (nitrite and nitrate). Recent investigations based on the methods of molecular ecology revealed that bacteria are responsible for nitrification in natural ecosystems. At the same time, data on the species composition of the nitrifiers in soil microbial communities are scarce. Soil samples collected in the forest and steppe areas of European Russia and the enrichment cultures of nitrifying bacteria isolated from these samples were used for molecular studies of the diversity of the amoA gene encoding the synthesis of the key enzyme of autotrophic ammonium oxidation. The nitrifying bacteria of the genera Nitrosospira and Nitrosovibrio were found in all the studied soils from natural biocenoses and agrocenoses.     

Spatially resolved correlative microscopy and microbial identification reveal dynamic depth- and mineral-dependent anabolic activity in salt marsh sediment

Coastal salt marshes are key sites of biogeochemical cycling and ideal systems in which to investigate the community structure of complex microbial communities. Here, we clarify structural–functional relationships among microorganisms and their mineralogical environment, revealing previously undescribed metabolic activity patterns and precise spatial arrangements within salt marsh sediment. Following 3.7-day in situ incubations with a non-canonical amino acid that was incorporated into new biomass, samples were resin-embedded and analysed by correlative fluorescence and electron microscopy to map the microscale arrangements of anabolically active and inactive organisms alongside mineral grains. Parallel sediment samples were examined by fluorescence-activated cell sorting and 16S rRNA gene sequencing to link anabolic activity to taxonomic identity. Both approaches demonstrated a rapid decline in the proportion of anabolically active cells with depth into salt marsh sediment, from ~60% in the top centimetre to 9.4%–22.4% between 2 and 10 cm. From the top to the bottom, the most prominent active community members shifted from sulfur cycling phototrophic consortia, to putative sulfate-reducing bacteria likely oxidizing organic compounds, to fermentative lineages. Correlative microscopy revealed more abundant (and more anabolically active) organisms around non-quartz minerals including rutile, orthoclase and plagioclase. Microbe–mineral relationships appear to be dynamic and context-dependent arbiters of biogeochemical cycling.     

Sulfur uptake in the ectomycorrhizal fungus Laccaria bicolor S238N

The importance of the ectomycorrhiza symbiosis for plant acquisition of phosphorus and nitrogen is well established whereas its contribution to sulfur nutrition is only marginally understood. In a first step to investigate the role of ectomycorrhiza in plant sulfur nutrition, we characterized sulfate and glutathione uptake in Laccaria bicolor. By studying the regulation of sulfate uptake in this ectomycorrhizal fungus, we found that in contrast to bacteria, yeast, and plants, sulfate uptake in L. bicolor was not feedback-inhibited by glutathione. On the other hand, sulfate uptake was increased by sulfur starvation as in other organisms. The activity of 3′-phosphoadenosine 5′-phosphosulfate reductase, the key enzyme of the assimilatory sulfate reduction pathway in fungi, was increased by sulfur starvation and decreased after treatment with glutathione revealing an uncoupling of sulfate uptake and reduction in the presence of reduced sulfur compounds. These results support the hypothesis that L. bicolor increases sulfate supply to the plant by extended sulfate uptake and the plant provides the ectomycorrhizal fungus with reduced sulfur.     

Reduced Sulfur in Ashes and Slags from the Gasification of Coals: Availability for Chemical and Microbial Oxidation

This study was initiated to determine if reduced sulfur contained in coal gasifier ash and slag was available for microbial and chemical oxidation because eventual large-quantity landfill disposal of these solid wastes is expected. Continuous application of distilled water to a column containing a high-sulfur-content (4% [wt/wt]) gasifier slag yielded leachates with high sulfate levels (1,300 mg of sulfate liter⁻¹) and low pH values (4.2). At the end of the experiment, a three-tube most-probable-number analysis indicated that the waste contained 1.3 × 10⁷ thiosulfate-oxidizing bacteria per g. Slag samples obtained aseptically from the column produced sulfate under both abiotic and biotic conditions when incubated in a mineral nutrient solution. Both microbial and chemical sulfate syntheses were greatly stimulated by the addition of thiosulfate to the slag-mineral nutrient solution. These results led to a test of microbial versus chemical sulfur oxidation in ashes and slags from five gasification processes. Sulfate production was measured in sterile (autoclaved) and nonsterile suspensions of the solid wastes in a mineral nutrient solution. These ashes and slags varied in sulfur content from 0.3 to 4.0% (wt/wt). Four of these wastes demonstrated both chemical (2.0 to 27 μg of sulfate g⁻¹ day⁻¹) and microbial (3.1 to 114 μg of sulfate g⁻¹ day⁻¹) sulfur oxidation. Obvious relationships between sulfur oxidation rate and either sulfur content or particle size distribution of the wastes were not immediately evident. We conclude that the sulfur contained in all but one waste is available for oxidation to sulfuric acid and that microorganisms play a partial role in this process.     

Concepts of sulfur,carbon, and nitrogen transformations in soil: evaluation by simulation modeling

The dynamics of sulfur immobilization and mineralization in soil were simulated to test hypotheses about their regulation by the availability of carbon and nitrogen. The concept of chemical bond classes was incorporated into the model to account for variation in composition of carbon, nitrogen, and sulfur compounds. Microbial biomass was differentiated into bacteria and fungi, and the element ratios of both groups were assumed to vary. Organic residues were divided between dead microbes plus microbial products, and the more labile fraction of stabilized soil organic matter. Concepts and hypotheses in the model were tested by applying it to data on microbial biomass, sulfate, nitrate, and CO₂ evolution obtained in laboratory incubations of two soils amended with sulfate and cellulose. An important mechanism of regulation tested in the model was the stimulation of sulfohydrolase enzyme production depending on sulfur stress in microbial biomass. The hypothesis that excess sulfate is stored as ester sulfate was supported by model dynamics.     

Exotic Earthworm Invasion and Microbial Biomass in Temperate Forest Soils

Invasion of north temperate forest soils by exotic earthworms has the potential to alter microbial biomass and activity over large areas of North America. We measured the distribution and activity of microbial biomass in forest stands invaded by earthworms and in adjacent stands lacking earthworms in sugar maple-dominated forests in two locations in New York State, USA: one with a history of cultivation and thin organic surface soil horizons (forest floors) and the other with no history of cultivation and a thick (3–5 cm) forest floor. Earthworm invasion greatly reduced pools of microbial biomass in the forest floor and increased pools in the mineral soil. Enrichment of the mineral soil was much more marked at the site with thick forest floors. The increase in microbial biomass carbon (C) and nitrogen (N) in the mineral soil at this site was larger than the decrease in the forest floor, resulting in a net increase in total soil profile microbial biomass in the invaded plots. There was an increase in respiration in the mineral soil at both sites, which is consistent with a movement of organic matter and microbial biomass into the mineral soil. However, N-cycle processes (mineralization and nitrification) did not increase along with respiration. It is likely that the earthworm-induced input of C into the mineral soil created a microbial sink for N, preventing an increase in net mineralization and nitrification and conserving N in the soil profile.     

Major contribution of sulfide-derived sulfur to the benthic food web in a large freshwater lake

In freshwater systems, contributions of chemosynthetic products by sulfur-oxidizing bacteria in sediments as nutritional resources in benthic food webs remain unclear, even though chemosynthetic products might be an important nutritional resource for benthic food webs in deep-sea hydrothermal vents and shallow marine systems. To study geochemical aspects of this trophic pathway, we sampled sediment cores and benthic animals at two sites (90 and 50 m water depths) in the largest freshwater (mesotrophic) lake in Japan: Lake Biwa. Stable carbon, nitrogen, and sulfur isotopes of the sediments and animals were measured to elucidate the sulfur nutritional resources for the benthic food web precisely by calculating the contributions of the incorporation of sulfide-derived sulfur to the biomass and of the biogeochemical sulfur cycle supporting the sulfur nutritional resource. The recovered sediment cores showed increases in ³⁴S-depleted sulfide at 5 cm sediment depth and showed low sulfide concentration with high δ³⁴S in deeper layers, suggesting an association of microbial activities with sulfate reduction and sulfide oxidation in the sediments. The sulfur-oxidizing bacteria may contribute to benthic animal biomass. Calculations based on the biomass, sulfur content, and contribution to sulfide-derived sulfur of each animal comprising the benthic food web revealed that 58%–67% of the total biomass sulfur in the benthic food web of Lake Biwa is occupied by sulfide-derived sulfur. Such a large contribution implies that the chemosynthetic products of sulfur-oxidizing bacteria are important nutritional resources supporting benthic food webs in the lake ecosystems, at least in terms of sulfur. The results present a new trophic pathway for sulfur that has been overlooked in lake ecosystems with low-sulfate concentrations.     

Elevated temperature shifts soil N cycling from microbial immobilization to enhanced mineralization,nitrification and denitrification across global terrestrial ecosystems

We assessed the response of soil microbial nitrogen (N) cycling and associated functional genes to elevated temperature at the global scale. A meta‐analysis of 1,270 observations from 134 publications indicated that elevated temperature decreased soil microbial biomass N and increased N mineralization rates, both in the presence and absence of plants. These findings infer that elevated temperature drives microbially mediated N cycling processes from dominance by anabolic to catabolic reaction processes. Elevated temperature increased soil nitrification and denitrification rates, leading to an increase in N₂O emissions of up to 227%, whether plants were present or not. Rates of N mineralization, denitrification and N₂O emission demonstrated significant positive relationships with rates of CO₂ emissions under elevated temperatures, suggesting that microbial N cycling processes were associated with enhanced microbial carbon (C) metabolism due to soil warming. The response in the abundance of relevant genes to elevated temperature was not always consistent with changes in N cycling processes. While elevated temperature increased the abundances of the nirS gene with plants and nosZ genes without plants, there was no effect on the abundances of the ammonia‐oxidizing archaea amoA gene, ammonia‐oxidizing bacteria amoA and nirK genes. This study provides the first global‐scale assessment demonstrating that elevated temperature shifts N cycling from microbial immobilization to enhanced mineralization, nitrification and denitrification in terrestrial ecosystems. These findings infer that elevated temperatures have a profound impact on global N cycling processes with implications of a positive feedback to global climate and emphasize the close linkage between soil microbial C and N cycling.     

双阳极室甲烷微生物燃料电池同步脱氮除硫性能及微生物群落分析

【背景】甲烷厌氧氧化(anaerobic oxidation of methane, AOM)包含反硝化型甲烷厌氧氧化和硫酸盐还原型甲烷厌氧氧化。目前,人们向水体中排放过量的含氮及含硫污染物,引起了严重的环境污染和生态破坏。【目的】利用甲烷厌氧氧化微生物燃料电池(microbial fuel cell, MFC)研究同步脱氮除硫耦合反应机理及反应过程中微生物的多样性信息。【方法】构建了3个微生物燃料电池(N-S-MFC、N-MFC、S-MFC),以甲烷作为唯一碳源,探究其同步脱氮除硫性能,并采用16S rRNA基因高通量测序技术对微生物群落结构进行分析。【结果】N-S-MFC中硝酸盐和硫酸盐的去除率分别为90.91%和18.46%。阳极室中微生物的相对丰度提高,与反硝化及硫酸盐还原菌相关的微生物大量富集,如门水平上拟杆菌门(Bacteroidota)、厚壁菌门(Firmicutes)和脱硫杆菌门(Desulfobacterota),同时属水平上Methylobacterium＿Methylorubrum、Methylocaldum、Methylomonas等常见的甲烷氧化菌增多。【结论...     

黄渤海海草分布区日本鳗草根际微生物群落结构特征及其功能分析

日本鳗草(Zostera japonica)是亚洲特有的海草种类,具有重要生态价值。近年来,黄渤海海草分布区中的日本鳗草海草床持续退化,引起了研究人员的广泛关注。【目的】基于根际微生物的分布与日本鳗草的健康生长密切相关的设想,本文旨在探究黄渤海海草分布区日本鳗草根际细菌群落结构多样性并分析其与海草健康生长的内在联系。【方法】选取黄渤海海草分布区中东营、威海、大连3个地点的日本鳗草根际与非草区表层沉积物,采用高通量测序技术(Illumina HiSeq PE300)解析根际微生物群落特征,并结合相关环境参数分析其环境功能。【结果】日本鳗草根际表层沉积物中主要存在的细菌类群有:变形菌门(Proteobacteria)所占比例为41.1%,蓝细菌门(Cyanobacteria)占15.4%,拟杆菌门(Bacteroidetes)占12.6%,放线菌门(Actinobacteria)占9.3%。不同地点之间以及样品类型(海草床根际与非根际)之间的微生物群落存在显著差异,主要表现为根际富含硫酸盐还原菌和固氮菌。环境因素:TN (total nitrogen)、TC (total carbon)、TOC (total organic carbon)、黏土(Clay)、砷(As)与根际群落组成与分布显著相关。【结论】从功能的角度来看,不同地点、不同样品类型之间的差异物种多与硫、氮代谢相关,硫酸盐还原菌对维持日本鳗草的生态健康起关键作用;日本鳗草根际微生物群落分布与环境因子、空间分布有一定相关性。