Responses of Microbial Communities in River to Atmospheric Deposition.

The responses of soil microbes to climatic and anthropological factors in the Tibetan grasslands

Almost all land plant species form a symbiosis with mycorrhizal fungi. These soil fungi provide nutrients and other services to plants in return for plant carbohydrates. The recent application of microbial metagenomics, metatranscriptomics, and metabolomics to plants and their immediate surroundings confirms the key role of mycorrhizal fungi, rhizosphere bacteria and fungi, and suggests a world of hitherto undiscovered interactions (van der Heijden et al., this issue, pp. 1406–1423). This novel knowledge is leading to a paradigm-shifting view: plants cannot be considered as isolated individuals any more, but as metaorganisms, or holobionts (Hacquard & Schadt, this issue, pp. 1424– 1430) encompassing an active microbial community re-programming host physiology (see Pozo et al., this issue, pp. 1431–1436). This bears tremendous implications for plant ecophysiology and evolution, plant breeding, crop management and sustainable ecosystem management.

Fungi are an important, yet often, neglected component of the aquatic microflora, and is responsible for primary decomposition and further processing of organic matter. By comparison, the ecological roles of terrestrial fungi have been well-studied, but the diversity and function of fungi that populate aquatic environments remain poorly understood. Here, the impact of urbanization on fungal diversity and community composition in the canal system of Suzhou was assessed by sequencing the internal transcribed spacer 1 (ITS1) region of the rRNA operon. It was amplified from environmental DNA that has been extracted from water samples and pre-deployed decomposing leaves collected from nine sampling locations (high, medium and low urbanization) over two seasons. The fungal diversity and community composition were determined by bioinformatic analysis of the large DNA sequence datasets generated to identify operational taxonomic units (OTUs) for phylogenetic assignment; over 1 million amplicons were sequenced from 36 samples. The alpha-diversity estimates showed high differences in fungal diversity between water and leaf samples, and winter versus summer. Higher numbers of fungal OTUs were identified in both water and leaf samples collected in the summer, and fungal diversity was also generally higher in water than on colonized leaves in both seasons. The fungal community on leaves was usually dominated by Ascomycetes, especially in winter, while water samples contained more diversity at phylum level with Chytridiomycetes often prominent, particularly in summer. At a genus level, a very high relative abundance of Alternaria on leaves was observed in winter at all locations, in contrast to very low abundance of this genus across all water samples. Fungal community composition also varied between sampling locations (i.e., urbanization); in cluster analysis, samples from high urbanization locations formed a distinct cluster, with medium and low urbanization samples clustering together or in some instances, separately. Redundancy analysis shed further light on the relationships between variation in fungal community composition and water physico-chemical properties. Fungal community diversity variation and correlation with different parameters is discussed in detail, but overall, the influence of season outweighed that of urbanization. This study is significant in cataloguing the impact of urbanization on fungal diversity to inform future restoration of urban canal systems on the importance of protecting the natural aquatic fungal flora.

Simple SummaryThe gut fungi assist the host in various physiological activities, homeostasis, immune responses, and growth. The diversity and community composition of gut fungi are driven by multiple factors, including diet, environmental exposure, habitat type, and seasonal migration. Migratory birds have a peculiar life cycle, so it is interesting to understand the ecological function of their “gut fungal microbiome.” Birds are exposed to variable diets, environments, and habitats amid seasonal migration. The hooded crane is known as a long-distance migratory bird, inhabiting both wintering and stopover grounds during seasonal migration. During migratory seasons, it inhabits various habitats and is exposed to variable environments. This study analyzed the shifts between gut fungal diversity and the community composition of the hooded crane at both wintering and stopover sites amid seasonal migration. The gut fungal alpha diversity exhibited a more significant change during winter than in fall and spring. The gut fungal community composition exhibited significant shifts across winter, fall, and spring (ANOSIM, p = 0.001). The pathogenic diversity and relative abundance showed significant differences during winter at the wintering site relative to fall and spring at the stopover site. Moreover, the pathogenic fungal community composition was significantly different during fall, winter, and spring. This work contributes to present essential knowledge about the gut fungal microbiome of hooded cranes amid seasonal migration. This study also implicated that conservation measures for hooded crane conservation should be applied, as the risk of cross-transmission of potential fungal pathogens might increase during seasonal migration.The “gut fungal microbiome” maintains the immune system, homeostasis, and various physiological functions of an organism. Different factors shape and affect gut fungal diversity and community composition, such as environment, habitat type, food resources, and seasons during migration. Wild birds amid migration are exposed to different habitats with different environments, available food resources, and seasons, which may substantially impact their gut fungal community composition and diversity. The hooded crane (Grus monacha) is a known migratory bird that migrates over long distances and is exposed to varied habitats with different environments and food types. We investigated the differences in gut fungal diversity and community composition between wintering and stopover sites amid three migratory seasons. We deduced the gut fungal pathogenic diversity and community composition during winter, fall, and spring by using high throughput sequencing (Illumina Mi-seq), and the internal transcribed region 2 (ITS2) was examined. Samples were collected from Shengjin Lake in the winter and Lindian during the fall and spring. The dominant fungal phyla found across the three seasons were Ascomycota, Basidiomycota, Zygomycota, and Rozellomycota. The gut fungal alpha diversity showed significant shifts during winter at the wintering site compared with the fall and spring seasons at the stopover site. The fungal community composition exhibited a significant change across the three seasons (ANOSIM p = 0.001). The results also demonstrated that the diversity and relative abundance of potential pathogens also showed divergence in winter compared to fall and spring. This study provides the basis for understanding the discrepancy in gut fungal diversity and community composition during migratory seasons at both wintering and stopover grounds. It also suggests that conservation measures should be applied to the conservation of hooded cranes and other wild birds, as the risk of cross-infection increases during seasonal migration.

Crop tree management (CTM) is a widely applicable silviculture technology that is used to improve the performance of individual trees. However, only little information is available about the effects of the CTM regime on the soil microbial community structure. We conducted a study to explore the effects of short-term (five years) CTM on the soil bacterial and fungal diversity, community composition, and structure in the 0–10 cm soil layer in a Larix gmelinii (Rupr.) Kuzen. plantation. We set out to investigate the differential response of bacterial and fungal communities to variations in soil properties mediated by short-term CTM. Compared with the control plots, the soil microbial biomass carbon and microbial biomass nitrogen in CTM increased significantly by 64.2% and 32.3%, respectively. CTM significantly promoted the content of soil organic carbon, dissolved organic carbon, and nitrate nitrogen, and reduced the content of dissolved organic nitrogen. CTM changed the Shannon and Simpson indices of soil fungi to a remarkable extent but had little effect on the α diversity of bacterial communities. The bacterial β diversity was more sensitive to CTM than fungi. The relative abundance of Verrucomicrobiae (the dominant class of soil bacteria) in CTM was significantly increased by 78.2%, while the relative abundance of Agaricomycetes (dominant class for soil fungi) was reduced by 43.3%. We observed a significantly increased number of unique OTUs for soil fungi in the CTM plots. Redundancy analysis showed that dissolved organic carbon, soil moisture, and total phosphorus content significantly affected the composition of bacterial communities, while soil dissolved organic nitrogen, C/N, and total phosphorus drove the high variation in fungal community composition. Overall, our results emphasize the divergent response of soil bacterial and fungal communities in Larix gmelinii plantations to short-term CTM. We must pay more attention to the functional role of soil microbiota in future forest management.

Fungal diversity and community composition are mainly related to soil and vegetation factors. However, the relative contribution of the different drivers remains largely unexplored, especially in subtropical forest ecosystems. We studied the fungal diversity and community composition of soils sampled from 12 comparative study plots representing three forest age classes (Young: 10–40 yrs; Medium: 40–80 yrs; Old: ≥80 yrs) in Gutianshan National Nature Reserve in South-eastern China. Soil fungal communities were assessed employing ITS rDNA pyrotag sequencing. Members of Basidiomycota and Ascomycota dominated the fungal community, with 22 putative ectomycorrhizal fungal families, where Russulaceae and Thelephoraceae were the most abundant taxa. Analysis of similarity showed that the fungal community composition significantly differed among the three forest age classes. Forest age class, elevation of the study plots, and soil organic carbon (SOC) were the most important factors shaping the fungal community composition. We found a significant correlation between plant and fungal communities at different taxonomic and functional group levels, including a strong relationship between ectomycorrhizal fungal and non-ectomycorrhizal plant communities. Our results suggest that in subtropical forests, plant species community composition is the main driver of the soil fungal diversity and community composition.

ABSTRACTDeciphering the relationships between microbes and their host plants is critical for a better understanding of microbial diversity maintenance and community stability. Here, we investigated fungal diversity and community assembly in the phyllosphere and rhizosphere of 13 tree species in a subtropical common-garden experiment. The results showed that fungal community structures significantly differed across compartments (leaf, root, and soil) and different tree species. Higher α-diversity was observed in the phyllosphere than in the roots and rhizospheric soil. Fungal community composition (β-diversity) was significantly affected by both compartment and species identity. The fungal community compositions were significantly correlated with soil pH in the roots and the soils as well as with soil nitrate and leaf total phosphorus in the leaves. We found that fungal community assemblies were mainly driven by deterministic processes, regardless of compartments. Moreover, host preference analyses indicated that stronger plant/fungus preferences occurred in leaves than in roots and soils. Our results highlight the differences in tree mycobiome between aboveground and belowground compartments and have important implications for the promotion of biodiversity conservation and management sustainability for the subtropical forest.IMPORTANCE Subtropical mountain forests are widely distributed in Southern China and are characterized by high biodiversity. The interactions between plants and fungi play pivotal roles in biodiversity maintenance and community stability. Nevertheless, knowledge of fungal diversity and of the community assembly patterns of woody plants is scarce. Here, we investigated fungal diversity and community assembly in the phyllosphere and rhizosphere of 13 tree species in a common-garden experiment. We found that both compartment and plant identity influenced fungal diversity, community, and guild compositions, while deterministic processes mainly governed the fungal community assembly, especially in the rhizospheric fungal communities. Our results demonstrate that tree leaves represent stronger host/fungi preferences than do roots and soils. Together, our findings enhance the understanding of the roles of compartment and plant identity in structuring fungal communities as well as promote fungal diversity maintenance in subtropical mountain forest ecosystems.

Different responses of soil bacterial and fungal communities to nitrogen deposition in a subtropical forest

In Europe, Pinus sylvestris and Picea abies are the most common coniferous tree species used in commercial forestry, which rely on high‐quality reproductive material for successful reforestation. Clear‐cut harvested forest sites are often replanted using tree seedlings, which are produced in forest nurseries using seeds from seed orchards. However, incidences of fungal diseases in seedling production show that a better knowledge of seedborne fungi, including fungal pathogens, is needed to manage diseases in forest nurseries. This study aimed to assess seedborne fungal communities associated with commercial seeds of P. abies, P. sylvestris and Larix sp. seeds originated from geographically separated regions in Sweden, Belarus, Finland and Poland. Fungal communities were obtained first from the seed surface and then from the seed tissue. These were analysed using high‐throughput sequencing of the ITS2 rDNA region. The results showed that fungal diversity and community composition differed between the seed surface and the seed tissue. Picea abies accommodated a higher fungal diversity than P. sylvestris. In addition, a strong host affinity of the fungal community composition on the seed surface and a weaker association in the seed tissue was found. Fungal communities on P. abies and P. sylvestris seed surface differed significantly between geographical regions, whereas no regional differences were found in the seed tissue. The seedborne fungal communities included a high proportion of plant pathogens, among which the most abundant were Sydowia polyspora (13.3%), Phoma herbarum (11.2%) and Sirococcus conigenus (3.8%). In conclusion, the results showed (a) characteristic fungal diversity and community composition between the seed surface and the seed tissue; (b) a host‐specific fungal community composition on the seed surface and in the seed tissue; (c) regional difference in fungal communities on P. abies and P. sylvestris seed surface, thus the movement of seeds between different regions can contribute to the spread of fungal diseases; and (d) the presence of a high incidence of seedborne fungal pathogens which suggest a potential need of preventative or control measures to reduce the occurrence of these fungi on the seed surface.

Investigating the response of soil microbial communities to nitrogen (N) deposition is critical to understanding biogeochemical processes and the sustainable development of forests. However, whether and to what extent different forms of N deposition affect soil microbial communities in temperate forests is not fully clear. In this work, a field experiment with three years of simulated nitrogen deposition was conducted in temperate forests. The glycine and urea were chosen as organic nitrogen (ON) source, while NH4NO3 was chosen as inorganic nitrogen (IN) source. Different ratios of ON to IN (CK = 0:0, Mix-1 = 10:0, Mix-2 = 7:3, Mix-3 = 5:5, Mix-4 = 3:7, Mix-5 = 0:10) were mixed and then used with equal total amounts of 10 kg·N·ha−1·a−1. We determined soil microbial diversity and community composition for bacteria and fungi (16S rRNA and ITS), and soil parameters. Different forms of N addition significantly changed the soil bacterial and fungal communities. Mixed N sources had a positive effect on soil bacterial diversity and a negative effect on fungal diversity. Bacterial and fungal community structures were significantly separated under different forms of N addition. Soil pH was the main factor affecting the change in fungal community structure, while bacterial community structure was mainly controlled by STN. We also found that Proteobacteria, Acidobacteriota, Basidiomycota and Ascomycota were the most abundant phyla, regardless of the form of N addition. RDA showed that C/P and NH4+ were the main factors driving the change in bacterial community composition, and C/P, pH and C/N were the main factors driving the change in fungal community composition. Our results indicate that different components of N deposition need to be considered when studying the effects of N deposition on soil microorganisms in terrestrial ecosystems.

Fertilizer input is one of the effective forest management practices, which improves soil nutrients and microbial community compositions and promotes forest productivity. However, few studies have explored the response of rhizosphere soil microbial communities to various fertilization regimes across seasonal dynamics. Here, we collected the rhizosphere soil samples from Phoebe bournei plantations to investigate the response of community assemblages and microbial interactions of the soil microbiome to the short-term application of four typical fertilizer practices (including chemical fertilizer (CF), organic fertilizer (OF), compound microbial fertilizer (CMF), and no fertilizer control (CK)). The amendments of organic fertilizer and compound microbial fertilizer altered the composition of rhizosphere soil bacterial and fungal communities, respectively. The fertilization regime significantly affected bacterial diversity rather than fungal diversity, and rhizosphere fungi responded more sensitively than bacteria to season. Fertilization-induced fungal networks were more complex than bacterial networks. Stochastic processes governed both rhizosphere soil bacterial and fungal communities, and drift and dispersal limitation dominated soil fungal and bacterial communities, respectively. Collectively, these findings demonstrate contrasting responses to community assemblages and interactions of rhizosphere bacteria and fungi to fertilizer practices. The application of organic fertilization strengthens microbial interactions and changes the succession of key taxa in the rhizosphere habitat.Key points• Fertilization altered the key taxa and microbial interaction• Organic fertilizer facilitated the turnover of rhizosphere microbial communities• Stochasticity governed soil fungal and bacterial community assembly

Fungi play an essential role in regulating the functioning of terrestrial ecosystems and are sensitive to climate change factors. Climate change incidents, such as N deposition and altered precipitation, create abiotic stress regarding the water use efficiency of soil and nutrient limitation impacting the activity of soil fungi. This study aimed to examine the combined effects of N fertilization and altered precipitation on soil fungal diversity and composition in the desert steppe. In the present study, we carried out a field experiment to assess the soil fungal diversity and composition of the desert steppe in response to N fertilizer (0 or 35 kg N ha−1 year−1) and precipitation changes (control, − 50% precipitation, or + 50% precipitation) in the desert steppe. The study was initiated in 2012, and plant and soil samples were collected after 5 years (August, 2017) of field treatments. High-throughput sequencing was applied to estimate the fungal diversity and composition. The soil fungal communities were dominated by Ascomycota (87.85% ± 1.26%), which primarily drove the fungal community composition. Decreased precipitation promoted strong shifts in fungal community composition under both N fertilizer levels. Increased precipitation significantly reduced Shannon-Wiener indices by 9.96%. The increasing relative abundances of fungal functional groups (lichenized saprotroph, animaland plant pathogens) resulted in a marked shift in fungal community composition from decreased precipitation to increased precipitation, which is attributed to the important role of the Ascomycota phylum in fungal communities. Structural equation modeling (SEM) indicated that C4 biomass was the predominant factor determining the Shannon-Wiener index for these fungi. Direct altered precipitation, indirect soil pH, and C4 biomass together controlled soil fungal community composition, with altered precipitation as the main driver. The interactive effects of N fertilizer and altered precipitation on grassland plant density, biomass, and soil properties may play an essential role in determining fungal diversity and community composition. Precipitation is a primary limiting factor that influences fungal community composition. Effects of N fertilizer on soil fungal community composition are highly dependent on changes in precipitation.

Warming exerts a stronger effect than nitrogen addition on the soil arbuscular mycorrhizal fungal community in a young subtropical Cunninghamia lanceolata plantation

PDF HTML阅读 XML下载 导出引用 引用提醒 施氮对森林生态系统AM真菌群落组成及多样性的影响 DOI: 10.5846/stxb202003120515 作者: 作者单位: 作者简介: 通讯作者: 中图分类号: 基金项目: 国家自然科学基金项目（41877050，31300446） Can understory nitrogen addition overestimate the effects of nitrogen deposition on arbuscular mycorrhizal fungal community? Author: Affiliation: Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:丛枝菌根（AM）真菌能够和绝大多数陆生植物形成互惠共生体，具有重要的生态功能。在氮（N）沉降日益严重的背景下，越来越多的土壤生态学家开始关注N沉降对AM真菌群落的影响，然而已有研究大多数集中在草地生态系统，对森林生态系统的关注相对较少，而在森林生态系统开展的模拟研究又多采用林下施N的方式，忽略了冠层发生的一系列生态过程，可能无法准确反映真实情形。依托鸡公山野外控制试验平台，采用高通量测序技术就不同施N方式（林下vs林冠）及速率对AM真菌alpha多样性和群落组成的影响进行了连续4 a的监测。试验综合考虑植被、坡向和坡度等因素，采用完全随机区组设计，包括4个区组（重复），每个区组随机设置5个样方，对应5个不同处理：对照（CK）、林冠施N 25 kg hm-2 a-1（CN25）和50 kg hm-2 a-1（CN50）、林下施N 25 kg hm-2 a-1（UN25）和50 kg hm-2 a-1（UN50）。结果发现，在目前的N素添加水平和时间尺度上，施N方式和施N速率对AM真菌的alpha多样性都没有显著影响，二者之间也无交互作用。然而，经过一年的试验处理，施N方式对AM真菌群落组成产生了轻微的影响，而施N速率有极显著的影响，且二者之间存在显著交互作用。当施N速率为25 kg hm-2 a-1时，林冠施N和对照相比差异不显著，而林下施N处理AM真菌群落组成与对照相比差异极显著，与林冠施N相比，差异也极显著；当施N速率为50 kg hm-2 a-1时，林冠施N与对照处理群落组成有略微差异（P=0.080），林下施N与林冠施N及对照处理相比AM真菌群落组成均没有显著变化。在接下来的三年中，施N方式和施N速率对AM真菌的群落组成都没有显著影响，二者之间也无显著交互作用。这说明在特定的施N速率和处理时间下，林下施N可能会高估自然N沉降对AM真菌群落组成的影响。随着处理时间的延长，不同处理下AM真菌群落有趋同的趋势，可能是因为AM真菌群落对N沉降产生了适应性。本研究评估了施N方式对森林生态系统AM真菌群落组成与结构的影响，在未来的研究中需要设定更多的N素梯度和更长的时间跨度，才能够更全面的认识N沉降的生态效应。 Abstract:Arbuscular mycorrhizal (AM) fungi can form symbiosis with most terrestrial plants and provide important ecological services. Under the intensified nitrogen (N) deposition, more and more soil ecologists pay attention to the impacts of N deposition on AM fungal community. However, most relevant studies were carried out in grassland ecosystems, while studies on forest ecosystem were very limited. Moreover, most simulation studies in forest ecosystems applied N to the forest floor, ignoring the canopy processes, may not accurately reflect the natural situations. We conducted a field experiment on the influence of N addition mode (understory vs canopy) and rate on AM fungi in a mixed deciduous forest of China. The experiment had a fully randomized block design with four blocks (replicates) and each block included five plots. Within each block, each plot was randomly assigned with one of the five treatments:ambient (CK), canopy addition of N at 25 (CN25) or 50 kg hm-2 a-1 (CN50), understory addition of N at 25 (UN25) or 50 kg hm-2 a-1 (UN50). AM fungal alpha diversity indices and community composition were determined by high-throughput sequencing. The results showed that under the experimental conditions, AM fungal richness and Shannon diversity indices were not significantly altered by N addition mode, rate or their interactions. However, after one year of experimental treatment, N application mode showed a marginal effect on AM fungal community composition, while N application rate showed an extremely significant effect, and the treatment interaction was also significant. At N addition rate of 25 kg hm-2 a-1, the difference between canopy N addition and control was not significant, while the AM fungal community composition was significantly changed by understory N addition. At N application rate of 50 kg hm-2.a-1, canopy addition of N slightly altered AM fungal community composition, but understory of N application did not change AM fungal community composition. In the next three years, N addition mode, rate or their interactions all showed no significant effects on AM fungal community composition. Overall, the results indicated that understory application of N may overestimate the effect of N deposition on the AM fungal community under natural conditions at certain N application rate and time scale. AM fungal communities under different treatments tend to converge over time, suggesting that AM fungal community may have adapted to N deposition over time. This study evaluated the effects of different N application modes on AM fungal community in forest ecosystem. We could have a more comprehensive understanding of the ecological impacts of N deposition by considering broader N gradients and longer observation period in future research. 参考文献 相似文献 引证文献

Cattle and poultry manure composting are often applied on agricultural lands but the fungal community composition before and after application in soils is still unclear. This study describes soil fungal diversity after manure applications contribute to the correct resource use of livestock and poultry manures. Fresh manure samples were obtained from 10 beef cow farms and 12 egg-laying poultry farms at five distinct phases of rearing. Surface soil samples were collected from vegetable plots within the farms after manure application at 15, 30 and 45 t hm-2 . Using high-throughput sequencing techniques, the ITS region was used to describe soil fungus populations. The fungal OTUs, Chao1 and ACE of cattle manure were relatively higher in the fattening stage (>12months), the OTUs and ACE of chicken manure were the highest in the initial laying stage (16-24 weeks). The fungal diversity indices of vegetable soils had no linear change after cow or chicken manure application compared with the control. Ascomycota (84.7% of total sequences), Neocallimastigomycota (9.69%) and Basidiomycota (4.6%) were the dominant phyla in cattle manure. Ascomycota (88.9%) also predominated in chicken manure followed by Basidiomycota (8.9%). Following both cattle and chicken manure applications, the abundance of Ascomycota decreased, whereas Basidiomycota and Chytridiomycota increased in the soils. None of the dominant genus increased or decreased linearly with the increase of cattle and chicken composting application rate. The fungal-dominant genera of the soils with and without manure composting application were mostly affected by soil pH and EC than manure. Pearson's correlation analysis revealed that organic matter, Cu and Hg contents were strongly linked to the fungal diversity and the abundance of specific taxa in cattle manure. In chicken manure, OM, TN and Zn were major factors controlling the fungal diversity and community composition. Soil pH, EC and Cu, Zn, Cd, Hg and As content had pronounced effects on the beneficial and pathogenic genus in soil with and without manure composting. Beneficial fungal genus such as Aspergillus, Plectosphaerella, Acremonium, Meyerozyma and fungal pathogenic such as Fusarium, Cladosporium, Verticillium were sensitive to properties (EC, pH, OM) and heavy metals (Cu, Zn, Hg) contents of the environment relatively. This study can serve as an applicable contribution helping in farms management (especially to cattle and poultry breeding) and improving their resource use of livestock and poultry manures. Soil heterogeneity rather than manure determines fungal communities in the vegetable fields, but we can encourage the sensible use of cattle and chicken manures in agroecosystems. This study will help farmers regulate the dosage of feed components which can increase the number of beneficial fungal genus or reduce the number of pathogenic fungal genus, improve their resource use of livestock and poultry manures and encourage the sensible use of cattle and chicken manures in agroecosystems.