18S rRNA Gene Variation among Common Airborne Fungi, and Development of Specific Oligonucleotide Probes for the Detection of Fungal Isolates

In this study, we sequenced 18S rRNA genes (rDNA) from 49 fungal strains representing 31 species from 15 genera. Most of these species are common airborne fungi and pathogens that may cause various public health concerns. Sequence analysis revealed distinct divergence between Zygomycota and Ascomycota. Within Ascomycota, several strongly supported clades were identified that facilitate the taxonomic placement of several little-studied fungi. Wallemia appeared as the group most diverged from all the other Ascomycota species. Based on the 18S rDNA sequence variation, 108 oligonucleotide probes were designed for each genus and species included in this study. After homology searches and DNA hybridization evaluations, 33 probes were verified as genus or species specific. The optimal hybridization temperatures to achieve the best specificity for these 33 probes were determined. These new probes can contribute to the molecular diagnostic research for environmental monitoring.     

Illumina高通量测序揭示艾比湖湿地6种盐生植物根际土壤真菌群落组成及多样性

【目的】通过研究新疆艾比湖湿地不同盐生植物根际土壤真菌的多样性和群落结构,为艾比湖湿地退化恢复工作和真菌深入研究提供理论支持。【方法】利用高通量测序技术对真菌扩增子ITS1区进行测定,从而分析艾比湖湿地6种盐生植物根际土壤真菌群落多样性,并结合相关土壤理化因子分析环境与真菌群落多样性和丰富度的关联。【结果】艾比湖湿地6种盐生植物根际土壤真菌群落多样性及丰富度存在差异,碱蓬根际土壤真菌多样性最高,芦苇根际土壤真菌群落丰富度最高。真菌群落组成分析表明,土壤样品中真菌菌落主要隶属于子囊菌门(Ascomycota)和担子菌门(Basidiomycota),其中子囊菌门为主要优势菌门;链格孢霉属(Alternaria)是6种植物共有的优势菌属,但是其在不同植物之间的丰度存在差异,在戟叶鹅绒藤中的丰度最高,在准噶尔大戟中的丰度最低。pH与真菌多样性呈显著负相关,全磷(TP)与真菌群落丰富度呈显著正相关,pH、电导率(EC)和有机质(OM)对优势菌属的影响最大。【结论】艾比湖湿地6种盐生植物根际土壤真菌群落组成及多样性具有显著差异,碱蓬和芦苇根际土壤真菌的多样性和丰度高于其他植物,子囊菌门和链格孢霉...     

Impact of mercury on denitrification and denitrifying microbial communities in nitrate enrichments of subsurface sediments

The contamination of groundwater with mercury (Hg) is an increasing problem worldwide. Yet, little is known about the interactions of Hg with microorganisms and their processes in subsurface environments. We tested the impact of Hg on denitrification in nitrate reducing enrichment cultures derived from subsurface sediments from the Oak Ridge Integrated Field Research Challenge site, where nitrate is a major contaminant and where bioremediation efforts are in progress. We observed an inverse relationship between Hg concentrations and onset and rates of denitrification in nitrate enrichment cultures containing between 53 and 1.1 μM of inorganic Hg; higher Hg concentrations increasingly extended the time to onset of denitrification and inhibited denitrification rates. Microbial community complexity, as indicated by terminal restriction fragment length polymorphism (tRFLP) analysis of the 16S rRNA genes, declined with increasing Hg concentrations; at the 312 nM Hg treatment, a single tRFLP peak was detected representing a culture of Bradyrhizobium sp. that possessed the merA gene indicating a potential for Hg reduction. A culture identified as Bradyrhizobium sp. strain FRC01 with an identical 16S rRNA sequence to that of the enriched peak in the tRFLP patterns, reduced Hg(II) to Hg(0) and carried merA whose amino acid sequence has 97 % identity to merA from the Proteobacteria and Firmicutes. This study demonstrates that in subsurface sediment incubations, Hg may inhibit denitrification and that inhibition may be alleviated when Hg resistant denitrifying Bradyrhizobium spp. detoxify Hg by its reduction to the volatile elemental form.     

Soil Formate Regulates the Fungal Nitrous Oxide Emission Pathway

Fungal activity is a major driver in the global nitrogen cycle, and mounting evidence suggests that fungal denitrification activity contributes significantly to soil emissions of the greenhouse gas nitrous oxide (N₂O). The metabolic pathway and oxygen requirement for fungal denitrification are different from those for bacterial denitrification. We hypothesized that the soil N₂O emission from fungi is formate and O₂ dependent and that land use and landforms could influence the proportion of N₂O coming from fungi. Using substrate-induced respiration inhibition under anaerobic and aerobic conditions in combination with ¹⁵N gas analysis, we found that formate and hypoxia (versus anaerobiosis) were essential for the fungal reduction of ¹⁵N-labeled nitrate to ¹⁵N₂O. As much as 65% of soil-emitted N₂O was attributable to fungi; however, this was found only in soils from water-accumulating landforms. From these results, we hypothesize that plant root exudates could affect N₂O production from fungi via the proposed formate-dependent pathway.     

Studies toward the comprehension of fungal-macroalgae interaction in cold marine regions from a biotechnological perspective

In marine ecosystems, macroalgae are the habitat for several microorganisms, fungi being among them. In the Antarctic benthic coastal ecosystem, macroalgae play a key role in organic matter cycling. In this study, 13 different macroalgae from Potter Cove and surrounding areas were sampled and 48 fungal isolates were obtained from six species, four Rhodophyta Ballia callitricha, Gigartina skottsbergii, Neuroglossum delesseriae and Palmaria decipiens, and two Phaeophyceae: Adenocystis utricularis and Ascoseira mirabilis. Fungal isolates mostly belonged to the Ascomycota phylum (Antarctomyces, Cadophora, Cladosporium, Penicillium, Phialocephala, and Pseudogymnoascus) and only one to the phylum Mucoromycota. Two of the isolates could not be identified to genus level, implying that Antarctica is a source of probable novel fungal taxa with enormous bioprospecting and biotechnological potential. 73% of the fungal isolates were moderate eurypsychrophilic (they grew at 5–25 °C), 12.5% were eurypsychrophilic and grew in the whole range, 12.5% of the isolates were narrow eurypsychrophilic (growth at 15–25 °C), and Mucoromycota AUe4 was classified as stenopsychrophilic as it grew at 5–15 °C. Organic extracts of seven macroalgae from which no fungal growth was obtained (three red algae Georgiella confluens, Gymnogongrus turquetii, Plocamium cartlagineum, and four brown algae Desmarestia anceps, D. Antarctica, Desmarestia menziesii, Himantothallus grandifolius) were tested against representative fungi of the genera isolated in this work. All extracts presented fungal inhibition, those from Plocamium cartilagineum and G. turquetii showed the best results, and for most of these macroalgae, this represents the first report of antifungal activity and constitute a promising source of compounds for future evaluation.     

象山港硅藻赤潮过程中真菌群落演替及互作特征

[背景] 近岸海域赤潮的发生能显著改变包括真菌在内的微生物群落组成,进而影响海洋中碳氮元素循环。真菌是海洋中重要的分解者,但赤潮过程对真菌群落的影响少有报道。[目的] 探明赤潮过程对真菌群落的影响,对进一步阐释赤潮对生态系统中物质循环的影响具有重要意义。[方法] 针对2017年春季象山港硅藻赤潮,对真菌内源转录间隔区1（Internally Transcribed Spacer 1,ITS1）序列进行高通量测序,研究赤潮过程中真菌群落响应及共现性特征。[结果] 真菌群落的α多样性指数在赤潮暴发的各阶段差异显著,而且均与磷酸盐、硝酸盐和亚硝酸盐有显著相关性（P<0.05）。子囊菌门（Ascomycota,90.2%）和担子菌门（Basidiomycota,8.27%）是本次硅藻赤潮的优势菌门,其中子囊菌门遍布赤潮暴发的4个阶段;锤舌菌纲（Leotiomycetes,16.1%）和散囊菌纲（Eurotiomycetes,9.3%）是纲水平上的主要优势类群。赤潮暴发过程中硝酸盐、亚硝酸盐、磷酸盐和温度等环境因素的改变,驱动真菌群落组成及结构发生显著变化。Helotiales、Eurotiales、Xylariales、Sacc haromycetales和Agaricostilbales构成了真菌群落共现网络的主体。[结论] 真菌群落在赤潮的各阶段具有显著的演替特征,赤潮藻生消是引起真菌群落演替的主要因素,但是环境因子也扮演着重要角色。赤潮过程中,真菌群落同类群内的互作要强于不同类群间的互作,这对维持群落的稳定性具有重要意义。     

Plant and Fungal Diversity in Gut Microbiota as Revealed by Molecular and Culture Investigations

Background

Few studies describing eukaryotic communities in the human gut microbiota have been published. The objective of this study was to investigate comprehensively the repertoire of plant and fungal species in the gut microbiota of an obese patient.

Methodology/Principal Findings

A stool specimen was collected from a 27-year-old Caucasian woman with a body mass index of 48.9 who was living in Marseille, France. Plant and fungal species were identified using a PCR-based method incorporating 25 primer pairs specific for each eukaryotic phylum and universal eukaryotic primers targeting 18S rRNA, internal transcribed spacer (ITS) and a chloroplast gene. The PCR products amplified using these primers were cloned and sequenced. Three different culture media were used to isolate fungi, and these cultured fungi were further identified by ITS sequencing. A total of 37 eukaryotic species were identified, including a Diatoms (Blastocystis sp.) species, 18 plant species from the Streptophyta phylum and 18 fungal species from the Ascomycota, Basidiomycota and Chytridiocomycota phyla. Cultures yielded 16 fungal species, while PCR-sequencing identified 7 fungal species. Of these 7 species of fungi, 5 were also identified by culture. Twenty-one eukaryotic species were discovered for the first time in human gut microbiota, including 8 fungi (Aspergillus flavipes, Beauveria bassiana, Isaria farinosa, Penicillium brevicompactum, Penicillium dipodomyicola, Penicillium camemberti, Climacocystis sp. and Malassezia restricta). Many fungal species apparently originated from food, as did 11 plant species. However, four plant species (Atractylodes japonica, Fibraurea tinctoria, Angelica anomala, Mitella nuda) are used as medicinal plants.

Conclusions/Significance

Investigating the eukaryotic components of gut microbiota may help us to understand their role in human health.     

Kinetic Explanation for Accumulation of Nitrite, Nitric Oxide, and Nitrous Oxide During Bacterial Denitrification

The kinetics of denitrification and the causes of nitrite and nitrous oxide accumulation were examined in resting cell suspensions of three denitrifiers. An Alcaligenes species and a Pseudomonas fluorescens isolate characteristically accumulated nitrite when reducing nitrate; a Flavobacterium isolate did not. Nitrate did not inhibit nitrite reduction in cultures grown with tungstate to prevent formation of an active nitrate reductase; rather, accumulation of nitrite seemed to depend on the relative rates of nitrate and nitrite reduction. Each isolate rapidly reduced nitrous oxide even when nitrate or nitrite had been included in the incubation mixture. Nitrate also did not inhibit nitrous oxide reduction in Alcaligenes odorans, an organism incapable of nitrate reduction. Thus, added nitrate or nitrite does not always cause nitrous oxide accumulation, as has often been reported for denitrifying soils. All strains produced small amounts of nitric oxide during denitrification in a pattern suggesting that nitric oxide was also under kinetic control similar to that of nitrite and nitrous oxide. Apparent K_m values for nitrate and nitrite reduction were 15 μM or less for each isolate. The K_m value for nitrous oxide reduction by Flavobacterium sp. was 0.5 μM. Numerical solutions to a mathematical model of denitrification based on Michaelis-Menten kinetics showed that differences in reduction rates of the nitrogenous compounds were sufficient to account for the observed patterns of nitrite, nitric oxide, and nitrous oxide accumulation. Addition of oxygen inhibited gas production from ¹³NO₃⁻ by Alcaligenes sp. and P. fluorescens, but it did not reduce gas production by Flavobacterium sp. However, all three isolates produced higher ratios of nitrous oxide to dinitrogen as the oxygen tension increased. Inclusion of oxygen in the model as a nonspecific inhibitor of each step in denitrification resulted in decreased gas production but increased ratios of nitrous oxide to dinitrogen, as observed experimentally. The simplicity of this kinetic model of denitrification and its ability to unify disparate observations should make the model a useful guide in research on the physiology of denitrifier response to environmental effectors.     

Effects of phenolic acids from ginseng rhizosphere on soil fungi structure,richness and diversity in consecutive monoculturing of ginseng

Ginseng yield and quality are seriously compromised by consecutive monoculturing in northeastern China. The imbalance of soil fungi communities and autotoxicity of ginseng are the major factors in consecutive monoculturing ginseng crops. Soil fungal communities were identified using Illumina MiSeq sequencing, applied to soils that consecutively cultured ginseng (CCG) for six years and new forest soil (NFS), or receiving application of phenolic acids (PAs). The CCG field received five treatments with five different phenolic acids, including gallic acid (GA), salicylic acid (SA), 3-phenylpropionic acid (3-PA), benzoic acid (BA) and cinnamic acid (CA), which were detected from ginseng rhizosphere in consecutive cropping soil. Fungal richness, fungi diversity, community composition, relative taxon abundances, root rot disease, and growth rate were compared among the different treatments. 579 fungal operational taxonomic units at 97% ITS sequence identity were found among 201,617 sequence reads derived from 18 separate soil samples. Members of the phylum Ascomycota dominated the soil fungal communities, and putative pathogens, such as Fusarium, Gibberella and Nectriaceae_unclassified which may include the abundant sexual morph of Cylindrocarpon destructans, showed higher relative abundances in the CCG fields. Compared to the CCG and NFS fields, PAs (except CA) enhanced the fungi richness and decreased fungi diversity. Cluster analysis indicated that the PAs (except CA) changed the fungi structure in a uniform way. PAs stimulate root rot disease and enhance disease severity, restricting plant growth. The results suggest that the PAs (except CA) may enhance the fungi richness, decrease the fungi diversity and changed the fungi structure to increase fungal pathogen loads, which could explain the declined yield and quality of ginseng in consecutively monocultured ginseng crops.     

Acetylene inhibition technique underestimates in situ denitrification rates in intact cores of freshwater sediment

Abstract Denitrification in intact sediment cores was measured by the acetylene inhibition technique and compared with the nitrate flux between water and sediment. Less than half of the nitrate-N consumed by the sediment could be recovered as nitrous oxide-N. The low recovery rate of nitrous oxide from intact sediment cores indicated losses of nitrous oxide by diffusion down to nitrate-free sediment layers, where reduction of nitrous oxide may take place. In sediment slurries 100% of nitrate-N could be recovered as nitrous oxide-N as long as the nitrate concentration in the liquid phase was above 10 μM. Nitrous oxide added to nitrate-free sediment slurries was reduced regardless of whether acetylene was present or not. Therefore denitrification may be significantly underestimated by this method.     

Temporal shifts of fungal communities in the rhizosphere and on tubers in potato fields

Soil fungal communities perform important ecological roles determining, at least in part, agricultural productivity. This study aimed at examining the fungal community dynamics in the potato rhizosphere across different development stages in two consecutive growing seasons (winter and summer). Microbial fingerprinting of rhizosphere soil samples collected at pre-planting, tuber initiation, flowering and at senescence was performed using ARISA in conjunction with Next Generation Sequencing (Illumina MiSeq). The epiphytic fungal communities on tubers at harvest were also investigated. Alpha-diversity was stable over time within and across the two seasons. In contrast, rhizospheric fungal community structure and composition were different between the two seasons and in the different plant growth stages within a given season, indicating the significance of the rhizosphere in shaping microbial communities. The phylum Ascomycota was dominant in the potato fungal rhizosphere, with Operational Taxonomic Units (OTUs) belonging to the genus Peyronellaea being the most abundant in all samples. Important fungal pathogens of potato, together with potential biological control agents and saprophytic species, were identified as indicator OTUs at different plant growth stages. These findings indicate that potato rhizosphere fungal communities are functionally diverse, which may contribute to soil health.     

The response of denitrifiers in a sandy loam soil affected by a long-term fertilization to organic carbon and nitrate

The response of denitrifiers to carbon in the form of glucose (Glc-C) and nitrate (NO ₃ ⁻ -N) amendments was studied in four differently fertilized plots of sandy-loam soil. Two basically different characteristics of denitrification activity were determined: (1) potential denitrification measured as nitrous oxide production during 1-d incubation in the presence of acetylene, and (2) denitrifying enzyme activity determined in soil slurries as a N₂O production in the presence of acetylene and chloramphenicol during 1 h of incubation. Potential denitrification was strongly influenced by both Glc-C and NO ₃ ⁻ -N amendments in their various combinations, but was also affected by the fertilization practice. The response of denitrifiers to Glc-C and NO ₃ ⁻ -N was generally lower in unfertilized and surprisingly also in highly fertilized soils than in organically and moderately fertilized soils. Denitrifying enzyme activity was stimulated by the fertilization and was, in contrast to potential denitrification, the highest in highly fertilized soil. The results indicate that although active denitrifiers were present in a highly fertilized soil, their ability to develop under optimal conditions was decreased (being similar to that of denitrifiers in unfertilized soil). This suggests long-term changes in soil microbial community in a highly fertilized soil, presumably connected to changes in soil chemistry caused by fertilization.     

Fluidized-bed denitrification for mine waters. Part I: low pH and temperature operation

Mining often leads to nitrate and metal contamination of groundwater and water bodies. Denitrification of acidic water was investigated in two up-flow fluidized-bed reactors (FBR) and using batch assays. Bacterial communities were enriched on ethanol plus nitrate in the FBRs. Initially, the effects of temperature, low-pH and ethanol/nitrate on denitrification were revealed. Batch assays showed that pH 4.8 was inhibitory to denitrification, whereas FBR characteristics permitted denitrification even at feed pH of 2.5 and at 7–8 °C. Nitrate and ethanol were removed and the feed pH was neutralized, provided that ethanol was supplied in excess to nitrate. Subsequently, Fe(II) and Cu impact on denitrification was investigated within batch tests at pH 7. Iron supplementation up to 100 mg/L resulted in iron oxidation and soluble concentrations ranging from 0.4 to 1.6 mg/L that stimulated denitrification. On the contrary, 0.7 mg/L of soluble Cu significantly slowed denitrification down resulting in about 45 % of inhibition in the first 8 h. Polymerase chain reaction—denaturant gradient gel electrophoresis demonstrated the co-existence of different denitrifying microbial consortia in FBRs. Dechloromonas denitrificans and Hydrogenophaga caeni were present in both FBRs and mainly responsible for nitrate reduction.     

The influence of nitrate concentration upon the end-products of nitrate dissimilation by bacteria in anaerobic salt marsh sediment

Abstract Experiments were carried out with slurries of saltmarsh sediment to which varying concentrations of nitrate were added. The acetylene blocking technique was used to measure denitrification by accumulation of nitrous oxide, while reduction of nitrate to nitrite and ammonium was also measured. There was good recovery of reduced nitrate and at the smallest concentration of nitrate used (250 μM) there was approximately equal reduction to either ammonium or nitrous oxide (denitrification). Nitrite was only a minor end-product of nitrate reduction. As the nitrate concentration was increased the proportion of the nitrate which was denitrified to nitrous oxide increased, to 83% at the greatest nitrate concentration used (2 mM), while reduction to ammonium correspondingly decreased. This change was attributed either to a greater competitiveness by the denitrifiers for nitrate as the ratio of electron donor to electron acceptor decreased; or to the increased production of nitrite rather than ammonium by fermentative bacteria under high nitrate, the nitrite then being reduced to nitrous oxide by denitrifying bacteria.     

Culturable fungal endophytes in roots of Enkianthus campanulatus (Ericaceae)

Roots of plants in the genus Enkianthus, which belongs to the earliest diverging lineage in the Ericaceae, are commonly colonized by arbuscular mycorrhizal (AM) fungi. We documented the community of fungal root endophytes associated with Enkianthus species using a culture-based method for better understanding the members of root-colonizing fungi, except for AM fungi. Fungal isolates were successfully obtained from 610 out of 3,599 (16.9 %) root segments. Molecular analysis of fungal cultures based on ribosomal internal transcribed spacer (ITS) sequences yielded 63 operational taxonomical units (OTUs: 97 % sequence similarity cutoff) from 315 representative isolates. Further phylogenetic analysis showed that most (296 isolates) belonged to Ascomycota and were either members of Helotiales (Dermataceae, Hyaloscyphaceae, Phialocephala and Rhizoscyphus ericae aggregate), Oidiodendron, or other Pezizomycotina. Twenty-three out of 63 OTUs, which mainly consisted of Leotiomycetes, showed high similarities with reference sequences derived from roots of other ericaceous plants such as Rhododendron. The results indicated that Enkianthus houses variable root mycobionts including putative endophytic and mycorrhizal fungi in addition to AM fungi.     

Bacterial and fungal taxon changes in soil microbial community composition induced by short-term biochar amendment in red oxidized loam soil

To take full advantage of biochar as a soil amendment, the objective of this study was to investigate the effects of biochar addition on soil bacterial and fungal diversity and community composition. Incubation experiments with a forest soil (a red oxidized loam soil) with and without biochar amendment were conducted for 96 days. The culture-independent molecular method was utilized to analyze soil bacterial and fungal species after the incubation experiments. Results showed that bacteria and fungi responded differently to the biochar addition during the short-term soil incubation. Twenty four and 18 bacterial genara were observed in the biochar amended and unamended soils, respectively, whereas 11 and 8 fungal genera were observed in the biochar amended and unamended soils, respectively. Microbial taxa analysis indicated that the biochar amendment resulted in significant shifts in both bacterial and fungal taxa during the incubation period. The shift for bacteria occurred at the genus and phylum levels, while for fungi only at the genus level. Specific taxa, such as Actinobacteria of bacteria and Trichoderma and Paecilomyces of fungi, were enriched in the biochar amended soil. The results reveal a pronounced impact of biochar on soil microbial community composition and an enrichment of key bacterial and fungal taxa in the soil during the short time period.     

Co-Occurring Anammox,Denitrification, and Codenitrification in Agricultural Soils

Anammox and denitrification mediated by bacteria are known to be the major microbial processes converting fixed N to N₂ gas in various ecosystems. Codenitrification and denitrification by fungi are additional pathways producing N₂ in soils. However, fungal codenitrification and denitrification have not been well investigated in agricultural soils. To evaluate bacterial and fungal processes contributing to N₂ production, molecular and ¹⁵N isotope analyses were conducted with soil samples collected at six different agricultural fields in the United States. Denitrifying and anammox bacterial abundances were measured based on quantitative PCR (qPCR) of nitrous oxide reductase (nosZ) and hydrazine oxidase (hzo) genes, respectively, while the internal transcribed spacer (ITS) of Fusarium oxysporum was quantified to estimate the abundance of codenitrifying and denitrifying fungi. ¹⁵N tracer incubation experiments with ¹⁵NO₃⁻ or ¹⁵NH₄⁺ addition were conducted to measure the N₂ production rates from anammox, denitrification, and codenitrification. Soil incubation experiments with antibiotic treatments were also used to differentiate between fungal and bacterial N₂ production rates in soil samples. Denitrifying bacteria were found to be the most abundant, followed by F. oxysporum based on the qPCR assays. The potential denitrification rates by bacteria and fungi ranged from 4.118 to 42.121 nmol N₂-N g⁻¹ day⁻¹, while the combined potential rates of anammox and codenitrification ranged from 2.796 to 147.711 nmol N₂-N g⁻¹ day⁻¹. Soil incubation experiments with antibiotics indicated that fungal codenitrification was the primary process contributing to N₂ production in the North Carolina soil. This study clearly demonstrates the importance of fungal processes in the agricultural N cycle.     

寒温带地区典型森林类型中外生菌根真菌多样性和群落组成及其影响因素

外生菌根(ECM)真菌可促进宿主植物对土壤中水分和营养的吸收,提高宿主植物的抗逆性及对环境的适应,在森林生态系统的物质循环中发挥了重要作用。为探明寒温带地区ECM真菌多样性和群落组成以及土壤理化因子对真菌群落组成的可能影响机制,采用高通量测序(Illumina Miseq)平台对大兴安岭4种典型森林类型白桦、樟子松、兴安落叶松和偃松的根围土壤ECM真菌群落组成进行了分析。结果表明,4种典型森林类型根围土壤中共获得167个ECM真菌可操作分类单元(OTUs),隶属于2个门、4个纲、10个目、24个科、36个属。在门水平上,担子菌门(Basidiomycota)真菌的相对丰度占96.4%,子囊菌门(Ascomycota)真菌占3.6%。在属水平上,红菇属(Russula,30.2%)、丝膜菌属(Cortinarius,17.1%)、Piloderma(9.6%)、棉革菌属(Tomentella,7.2%)、丝盖伞属(Inocybe,7.2%)和蜡壳耳属(Sebacina,6.2%)的相对丰度均>5.0%,是该地区的优势ECM真菌类群。不同森林类型的优势ECM真菌在属水平上的组成存在显...     

Denitrification in a nitrogen-limited stream ecosystem

Denitrification was measured in hyporheic, parafluvial, and bank sediments of Sycamore Creek, Arizona, a nitrogen-limited Sonoran Desert stream. We used three variations of the acetylene block technique to estimate denitrification rates, and compared these estimates to rates of nitrate production through nitrification. Subsurface sediments of Sycamore Creek are typically well-oxygenated, relatively low in nitrate, and low in organic carbon, and therefore are seemingly unlikely sites of denitrification. However, we found that denitrification potential (C & N amended, anaerobic incubations) was substantial, and even by our conservative estimates (unamended, oxic incubations and field chamber nitrous oxide accumulation), denitrification consumed 5–40% of nitrate produced by nitrification. We expected that denitrification would increase along hyporheic and parafluvial flowpaths as dissolved oxygen declined and nitrate increased. To the contrary, we found that denitrification was generally highest at the upstream ends of subsurface flowpaths where surface water had just entered the subsurface zone. This suggests that denitrifiers may be dependent on the import of surface-derived organic matter, resulting in highest denitrification rate at locations of surface-subsurface hydrologic exchange. Laboratory experiments showed that denitrification in Sycamore Creek sediments was primarily nitrogen limited and secondarily carbon limited, and was temperature dependent. Overall, the quantity of nitrate removed from the Sycamore Creek ecosystem via denitrification is significant given the nitrogen-limited status of this stream.     

Responses of bacterial and fungal communities to an elevation gradient in a subtropical montane forest of China

Bacteria and fungi are ecologically important contributors to various functioning of forest ecosystems. In this study, we examined simultaneously the bacterial and fungal distributions in response to elevation changes of a forest. By using clone library analysis from genomic DNA extracted from forest humic clay soils, the composition and diversity of bacterial and fungal communities were determined across an elevation gradient from low via medium to high, in a subtropical forest in the Mountain Lushan, China. Our results showed that soil water content and nutrient availability, specifically total carbon, differed significantly with elevation changes. Although the soil acidity did not differ significantly among the three sites, low pH (around 4) could be an important selection factor selecting for acidophilic Acidobacteria and Alphaproteobacteria, which were the most abundant bacterial clones. As the majority of the fungi recovered, both Basidiomycota and Ascomycota, and their relative abundance were most closely associated with the total carbon. Based on the Shannon–Weaver diversity index and ∫-libshuff analysis, the soil at medium elevation contained the highest diversity of bacteria compared with those at high and low elevations. However, it is difficult to predict overall fungal diversity along elevation. The extreme high soil moisture content which may lead to the formation of anaerobic microhabitats in the forest soils potentially reduces the overall bacterial and fungal diversity.