Host plant richness explains diversity of ectomycorrhizal fungi: Response to the comment of Tedersoo et al. (2014)

Exploring the relationships between the biodiversity of groups of interacting organisms yields insight into ecosystem stability and function (Hooper et al. 2000 ; Wardle 2006 ). We demonstrated positive relationships between host plant richness and ectomycorrhizal (EM) fungal diversity both in a field study in subtropical China (Gutianshan) and in a meta‐analysis of temperate and tropical studies (Gao et al. 2013 ). However, based on re‐evaluation of our data sets, Tedersoo et al. ( 2014 ) argue that the observed positive correlation between EM fungal richness and EM plant richness at Gutianshan and also in our metastudies was based mainly from (i) a sampling design with inconsistent species pool and (ii) poor data compilation for the meta‐analysis. Accordingly, we checked our data sets and repeated the analysis performed by Tedersoo et al. ( 2014 ). In contrast to Tedersoo et al. ( 2014 ), our re‐analysis still confirms a positive effect of plant richness on EM fungal diversity in Gutianshan, temperate and tropical ecosystems, respectively.     

Host plant genus-level diversity is the best predictor of ectomycorrhizal fungal diversity in a Chinese subtropical forest

Microbial diversity is generally far higher than plant diversity, but the relationship between microbial diversity and plant diversity remains enigmatic. To shed light on this problem, we examined the diversity of a key guild of root-associated microbes, that is, ectomycorrhizal (EM) fungi along a plant diversity gradient in a Chinese subtropical forest. The results indicated that EM fungal diversity was positively correlated with host plant diversity. Furthermore, this relationship was best predicted by host genus-level diversity, rather than species-level diversity or family-level diversity. The generality of this finding was extended beyond our study system through the analyses of 100 additional studies of EM fungal communities from tropical and temperate forests. Here as well, EM fungal lineage composition was significantly affected by EM plant diversity levels, and some EM fungal lineages were co-associated with some host plant genera. These results suggest a general diversity maintenance mechanism for host-specific microbes based on higher order host plant phylogenetic diversity.     

Mammal mycophagy and fungal spore dispersal across a steep environmental gradient in eastern Australia

We examined changes in the types of fungi consumed by six species of small mammals across a habitat gradient in north‐eastern New South Wales that graded from swamp, to woodland, to open forest and then to rainforest. All mammals ate some fungus, but only bush rats (Rattus fuscipes) regularly did so, and their diet included most of the fungal taxa that we identified across all mammals in the study. The composition of bush rat diet changed significantly with each change in habitat from woodland, to forest, to rainforest. In particular, there was a significant difference in the diets of rats caught either side of the open forest‐rainforest ecotone, which marks the change in fungal community from one dominated by ectomycorrhizal fungi, to a community dominated by arbuscular mycorrhizal fungi. Movement patterns of bush rats living around the open forest‐rainforest ecotone suggest that they transport fungal spores between these contrasting fungal communities. Therefore, bush rats have the potential, by way of spore dispersal, to influence the structure of vegetation communities.     

Spatial distribution of ectomycorrhizal mats in coniferous forests of the Pacific Northwest, USA

Ectomycorrhizal mats in forest soils have a wide global distribution and have been noted as potentially important elements in forest soil nutrient cycling. To elucidate the relationship between ectomycorrhizal mats and their environment, we undertook field studies and spatial analyses of mat distributions at different spatial scales.We used two experimental approaches to study mat-forming ectomycorrhizal fungi in coniferous forests of the Pacific Northwest in the United States. In the first approach, ectomycorrhizal mats and other forest floor features were mapped in 2 × 10 m plots and digitized into a geographical information system (GIS) for spatial pattern analysis. In order to examine larger-scale phenomena, a second approach involving other sites was taken; soil cores were taken along 30-m transects, and distance to the closest living potential host tree was calculated for each core.Mat patterns were studied at two scales: (1) within-stand level (i.e. variability attributed to distribution of other mat species, forest floor attributes, and understory vegetation); and (2) stand level (i.e. variability expressed along a successional gradient). Mat distribution was influenced by: (1) the proximity of one mat to another; (2) the distance from the mat to the closest living tree; (3) the density of living trees in a stand; and (4) the successional stage of the stand.Although GIS analysis indicated that mats of different morphologies did not physically overlap, there was a tendency for clustering of mats. No apparent correlations were observed between forest floor features and mats located within the 2 × 10 m grids. On the scale of tens of meters, mats decreased with distance from the closest potential host tree. Spatial patterns of mat distributions in harvested sites suggest that these mats may persist at least 2 years after their host trees have been cut. For Gautieria mats, total mat area, size, and frequency differed with stand age.This study has demonstrated the importance of both spatial scaling and forest stand age when the natural distribution of mycorrhizal fungi is examined. Results suggest the need for mat research directed at higher-order scales (e.g. stand and watershed) that will provide accurate information for managing forests to ensure their survival and normal function. ei]J H Graham     

Diversity and community structure of ectomycorrhizal mycorrhizal fungi in roots and rhizosphere soil of Abies koreana and Taxus cuspidata in Mt. Halla

In this study, the roots and rhizosphere soil of Abies koreana and Taxus cuspidata were collected from sites at two different altitudes on Mt. Halla. Ectomycorrhizal fungi (EMF) were identified by Illumina MiSeq sequencing. The proportion of EMF from the roots was 89% in A. koreana and 69% in T. cuspidata. Among EMF in rhizosphere soils, the genus Russula was the most abundant in roots of A. koreana (p < 0.05). The altitude did not affect the biodiversity of EMF communities but influenced fungal community composition. However, the host plants had the most significant effect on EMF communities. The result of the EMF community analysis showed that even if the EMF were isolated from the same altitudes, the EMF communities differed according to the host plant. The community similarity index of EMF in the roots of A. koreana was higher than that of T. cuspidata (p < 0.05). The results show that both altitude and host plants influenced the structure of EMF communities. Conifers inhabiting harsh sub-alpine environments rely strongly on symbiotic relationships with EMF. A. koreana is an endangered species with a higher host specificity of EMF and climate change vulnerability than T. cuspidata. This study provides insights into the EMF communities, which are symbionts of A. koreana, and our critical findings may be used to restore A. koreana.     

Analysis of bacterial and archaeal diversity in coastal microbial mats using massive parallel 16S rRNA gene tag sequencing

Coastal microbial mats are small-scale and largely closed ecosystems in which a plethora of different functional groups of microorganisms are responsible for the biogeochemical cycling of the elements. Coastal microbial mats play an important role in coastal protection and morphodynamics through stabilization of the sediments and by initiating the development of salt-marshes. Little is known about the bacterial and especially archaeal diversity and how it contributes to the ecological functioning of coastal microbial mats. Here, we analyzed three different types of coastal microbial mats that are located along a tidal gradient and can be characterized as marine (ST2), brackish (ST3) and freshwater (ST3) systems. The mats were sampled during three different seasons and subjected to massive parallel tag sequencing of the V6 region of the 16S rRNA genes of Bacteria and Archaea. Sequence analysis revealed that the mats are among the most diverse marine ecosystems studied so far and consist of several novel taxonomic levels ranging from classes to species. The diversity between the different mat types was far more pronounced than the changes between the different seasons at one location. The archaeal community for these mats have not been studied before and revealed a strong reaction on a short period of draught during summer resulting in a massive increase in halobacterial sequences, whereas the bacterial community was barely affected. We concluded that the community composition and the microbial diversity were intrinsic of the mat type and depend on the location along the tidal gradient indicating a relation with salinity.     

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...     

Association of ectomycorrhizal mats with Pacific yew and other understory trees in coniferous forests

This study was designed to determine whether ectomycorrhizal mats (ECM) are more likely to be present in soils at the base of common understory trees than in soils distant from trees and to determine whether occurrence of ECM is related to tree size. Three understory trees were studied: Pacific yew (Taxus brevifolia Nutt.), western hemlock (Tsuga heterophylla (Raf.)Sarg), and vine maple (Acer circinatum Pursh). The 12 sites studied represent a range of climatic conditions and management histories. More than 2,900 plots were surveyed over 18 months. The incidence of ECM was higher at the base of all three species than in control plots. Incidence of mats was also positively correlated with tree size. Saplings consistently had a lower incidence of ECM than did larger trees.Paper 3028 of the Forest Research Laboratory, Oregon State University, Corvallis     

连续三年夜间增温和施氮对云杉外生菌根及菌根真菌多样性的影响

以西南亚高山针叶林建群种粗枝云杉(Picea asperata)为研究对象,采用红外加热模拟增温结合外施氮肥(NH₄NO₃ 25 g N m^-2 a^-1)的方法,研究连续3a夜间增温和施肥对云杉幼苗外生菌根侵染率、土壤外生菌根真菌生物量及其群落多样性的影响。结果表明:夜间增温对云杉外生菌根侵染率的影响具有季节性及根级差异。夜间增温对春季(2011年5月)云杉1级根,夏季(2011年7月)和秋季(2010年10月)云杉2级根侵染率影响显著。除2011年7月1级根外,施氮对云杉1、2级根侵染率无显著影响。夜间增温对土壤中外生菌根真菌的生物量和群落多样性无显著影响,施氮及增温与施氮联合处理使土壤中外生菌根真菌生物量显著降低,但却提高了外生菌根真菌群落的多样性。这说明云杉幼苗外生菌根侵染率对温度较敏感,土壤外生菌根真菌生物量及其群落多样性对施氮较敏感。这为进一步研究该区域亚高山针叶林地下过程对全球气候变化的响应机制提供了科学依据。     

外生菌根真菌多样性的分布格局与维持机制研究进展

外生菌根(ectomycorrhiza,ECM)是由土壤真菌与陆地植物根系形成的一种互惠共生体。ECM真菌从寄主植物中获取生长所需的碳源,同时促进寄主吸收氮、磷等矿物营养物质和水分。作为生态系统的重要组分,ECM真菌在生态系统的演替和多样性维持中发挥着重要的作用,因而揭示ECM真菌多样性的分布格局与维持机制是生物多样性与生态系统功能研究的热点领域之一。本文对ECM真菌多样性的最新研究进展进行了综合分析,相关研究显示,从热带到亚热带、温带森林,每种寄主植物上ECM真菌的平均物种数逐渐升高。扩散和选择过程都影响ECM真菌的分布格局,其中扩散对ECM真菌分布的影响具有空间尺度依赖性,即在全球和局域尺度上,扩散对ECM真菌分布的影响较弱,而在区域和小尺度上很强。同时,在局域尺度上,扩散对ECM真菌的分布具有寄主植物优势度依赖性,即在寄主植物不占优势的生态系统中,扩散对ECM真菌的分布有明显作用;而在寄主植物占优势的生态系统中则无影响。植物、动物、微生物和非生物因素的选择也都影响ECM真菌的分布格局,其中在温带地区所有研究均表明选择对ECM真菌的分布有影响,但是在热带地区有的研究表明选择对ECM真菌的分布有影响,而有的研究则显示无影响。植物的多样性和生产力都能影响ECM真菌的多样性,其中在温带、亚热带和热带森林中寄主植物属的多样性决定ECM真菌多样性,而植物生产力多样性假说只在一些温带的研究中得到证实。未来的研究重点应关注全球尺度,特别是在全球气候变化背景下的ECM真菌多样性的分布格局、维持机制及其生态系统功能等方面。     

DNA from soil mirrors plant taxonomic and growth form diversity

Ecosystems across the globe are threatened by climate change and human activities. New rapid survey approaches for monitoring biodiversity would greatly advance assessment and understanding of these threats. Taking advantage of next-generation DNA sequencing, we tested an approach we call metabarcoding: high-throughput and simultaneous taxa identification based on a very short (usually <100 base pairs) but informative DNA fragment. Short DNA fragments allow the use of degraded DNA from environmental samples. All analyses included amplification using plant-specific versatile primers, sequencing and estimation of taxonomic diversity. We tested in three steps whether degraded DNA from dead material in soil has the potential of efficiently assessing biodiversity in different biomes. First, soil DNA from eight boreal plant communities located in two different vegetation types (meadow and heath) was amplified. Plant diversity detected from boreal soil was highly consistent with plant taxonomic and growth form diversity estimated from conventional above-ground surveys. Second, we assessed DNA persistence using samples from formerly cultivated soils in temperate environments. We found that the number of crop DNA sequences retrieved strongly varied with years since last cultivation, and crop sequences were absent from nearby, uncultivated plots. Third, we assessed the universal applicability of DNA metabarcoding using soil samples from tropical environments: a large proportion of species and families from the study site were efficiently recovered. The results open unprecedented opportunities for large-scale DNA-based biodiversity studies across a range of taxonomic groups using standardized metabarcoding approaches.     

DNA-based fungal diversity in Madagascar and arrival of the ectomycorrhizal fungi to the island

Madagascar is known for its high diversity and endemism of fauna and flora. Fungi, however, have been largely overlooked in diversity and evolution studies on the island, and whether fungi exhibit the same patterns as animals and plants has yet to be further examined. We collected fungal sporocarps and ectomycorrhizal (EcM) roots during three opportunistic surveys in five forests in Madagascar and generated a dataset of fungal Internal Transcribed Spacer (ITS) DNA sequences. We analyzed them together with all publicly available fungal ITS DNA sequences and identified 620 Operational Taxonomic Units (OTUs) from Madagascar, 10% of which contained only sequences from our surveys. Two hundred and ninety-two OTUs belonged to EcM species with /russula-lactarius, /boletus, /tomentella-telephora, /cortinarius, and /amanita being the most abundant EcM lineages. Overall, 60% of all fungi and 81% of the EcM species from Madagascar appear to be endemic. We conducted a phylogenetic analysis using all the OTUs in Amanitaceae, Boletaceae, and Russulaceae families to elucidate their relative timing of arrival in Madagascar. We found that most EcM species from Madagascar in the three families diverged less than 22 million years ago (mya), long after the separation of India and Madagascar (88 mya), which is consistent with a dispersal mediated process of arrival to the island. Our study provides the first comprehensive view of the overall DNA-based fungal diversity in Madagascar and the current state of knowledge of EcM fungi based on DNA sequences, useful for further ecological and evolutionary studies. Abstract in Malagasy is available with online material.     

呼伦贝尔沙地樟子松外生菌根真菌多样性

沙地樟子松是我国北方重要的防风固沙造林树种,也是一种典型的外生菌根依赖型树种。为揭示呼伦贝尔沙地樟子松外生菌根真菌多样性,以中龄、近熟、成熟3个龄组沙地樟子松人工林和沙地樟子松天然林为研究对象,采用野外调查和分子生物学相结合的研究方法,鉴定分析沙地樟子松外生菌根真菌种群特征。研究结果表明：（1）呼伦贝尔沙地樟子松外生菌根真菌共有10个OTU属于子囊菌,48个OTU属于担子菌,隶属于21科25属。（2）天然林优势菌为糙缘腺革菌属Amphinema、丝膜菌属Cortinarius和乳牛肝菌属Suillus,人工林优势菌为乳牛肝菌属,其余菌种相对丰度随着林龄变化波动较大。（3）天然林与人工林外生菌根真菌种群Shannon、Simpson和Pielou指数存在显著差异（P<0.05）,人工林间alpha多样性指数差异不显著（P>0.05）。（4）呼伦贝尔沙地樟子松天然林和人工林外生菌根真菌种群组成存在较大差异,其中近熟林的外生菌根真菌群落组成与天然林的最为接近。     

High richness of ectomycorrhizal fungi and low host specificity in a coastal sand dune ecosystem revealed by network analysis

Ectomycorrhizal (EM) fungi are ubiquitous in temperate and boreal forests, comprising over 20,000 species forming root symbiotic associations with Pinaceae and woody angiosperms. As much as 100 different EM fungal species can coexist and interact with the same tree species, forming complex multispecies networks in soils. The degree of host specificity and structural properties of these interaction networks (e.g., nestedness and modularity) may influence plant and fungal community assembly and species coexistence, yet their structure has been little studied in northern coniferous forests, where trees depend on EM fungi for nutrient acquisition. We used high‐throughput sequencing to characterize the composition and diversity of bulk soil and root‐associated fungal communities in four co‐occurring Pinaceae in a relic foredune plain located at Îles de la Madeleine, Québec, Canada. We found high EM fungal richness across the four hosts, with a total of 200 EM operational taxonomic units (OTUs), mainly belonging to the Agaricomycetes. Network analysis revealed an antinested pattern in both bulk soil and roots EM fungal communities. However, there was no detectable modularity (i.e., subgroups of interacting species) in the interaction networks, indicating a low level of specificity in these EM associations. In addition, there were no differences in EM fungal OTU richness or community structure among the four tree species. Limited shared resources and competitive exclusion typically restrict the number of taxa coexisting within the same niche. As such, our finding of high EM fungal richness and low host specificity highlights the need for further studies to determine the mechanisms enabling such a large number of EM fungal species to coexist locally on the same hosts.     

Temporal variation in temperature and rainfall differentially affects ectomycorrhizal colonization at two contrasting sites

We examined the roles that seasonal shifts in precipitation and temperature played in the ectomycorrhizal (ECM) colonization of pinyon pine ( Pinus edulis Engelm.) at two contrasting sites in northern Arizona. Pinyons growing in ash and cinder soils experienced much greater water and nutrient stress than pinyons growing nearby in sandy-loam soils. Over a one year period, we obtained monthly measurements of ECM colonization, root zone soil moisture and temperature, and air temperature and precipitation. Four major patterns emerged. Firstly, although climate as measured by ambient temperature and precipitation did not vary between the two sites, soil temperature was significantly higher and soil moisture significantly lower at the cinder site than at the sandy-loam site. Secondly, ECM colonization was significantly higher at the cinder site for 5 of 12 months. Thirdly, although nearly 70% of the variation in ECM colonization of pinyons growing in cinder soil was predicted by a combination of soil moisture and soil temperature, these same variables had little predictive power for pinyons growing in sandy-loam soils. Air temperature and precipitation were also significantly correlated with ECM colonization at the cinder site but not the sandy-loam site. Fourthly, a watering experiment showed that ECM colonization significantly increased with supplemental water at the cinder site, but not at the sandy-loam site. Thus, in two sites that did not differ in plant community or climate, ectomycorrhizas in cinder soils were far more sensitive to changes in moisture and temperature than ectomycorrhizas in sandy-loam soils.     

太行山片麻岩区栓皮栎外生菌根真菌多样性

以太行山片麻岩区栓皮栎Quercus variabilis为研究对象,利用形态学、常规测序与Illumina MiSeq高通量测序相结合的方法,调查并鉴定了与其共生的外生菌根真菌。最终共划分出18种栓皮栎外生菌根形态类型。高通量测序得到394个外生菌根真菌OTUs（operational taxonomic units）,隶属于11目23科30属。其中栓皮栎外生菌根核心菌群（core microbiome）共9属17个OTUs,总相对多度达65.16%。样地1与样地2中样本的多样性指数无明显差异,但非度量多维尺度分析（NMDS）表明核心菌群在2个样地中的分布不同,其中红菇属Russula、牛肝菌属Boletus、粉孢牛肝菌属Tylopilus、硬皮地星属Astraeus主要分布于位于阳坡的样地1,而空团菌属Cenococcum、小球孢盘菌属Sphaerosporella、锁瑚菌属Clavulina、丝盖伞属Inocybe主要分布于位于阴坡的样地2,毛革菌属Tomentella在两个样地的分布相似。     

毛乌素沙地樟子松外生菌根真菌多样性特征

【背景】外生菌根真菌(ectomycorrhizal fungi,ECMF)侵入林木根系形成外生菌根,是樟子松(Pinus sylvestris var. mongholica)适应环境变化和环境胁迫的重要途径。【目的】深入理解沙地樟子松人工林外生菌根真菌群落组成和多样性。【方法】以毛乌素沙地3个林龄(27、33和44 a)沙地樟子松人工林为研究对象,采用rDNA ITS区段PCR扩增测序方法鉴定分析沙地樟子松外生菌根真菌群落组成并计算多样性指数。【结果】毛乌素沙地樟子松共获得56个外生菌根真菌OTU,隶属于2门3纲8目15科21属,优势属为棉革菌属(Tomentella)、地孔菌属(Geopora)和阿太菌属(Amphinema)。27 a人工林外生菌根真菌丰富度指数最高,33 a人工林ECMF的α多样性指数最高,但不同林龄之间不存在显著差异(P>0.05)。不同林龄沙地樟子松ECMF群落组成存在差异,地孔菌属、棉革菌属、Delastria和Mallocybe的动态变化是造成群落组成差异的主要原因。【结论】毛乌素沙地樟子松人工林外生菌根真菌群落组成较为丰富,该研究区的群落组成可能比多样性更能体现外生菌根真菌群落随林龄的动态变化,伴随着林木的生长成熟,部分功能性外生菌根真菌的动态变化可能与沙地樟子松人工林退化存在密切联系,有待进一步研究。     

In and out of refugia: historical patterns of diversity and demography in the North American Caesar's mushroom species complex

Some of the effects of past climate dynamics on plant and animal diversity make‐up have been relatively well studied, but to less extent in fungi. Pleistocene refugia are thought to harbour high biological diversity (i.e. phylogenetic lineages and genetic diversity), mainly as a product of increased reproductive isolation and allele conservation. In addition, high extinction rates and genetic erosion are expected in previously glaciated regions. Some of the consequences of past climate dynamics might involve changes in range and population size that can result in divergence and incipient or cryptic speciation. Many of these dynamic processes and patterns can be inferred through phylogenetic and coalescent methods. In this study, we first delimit species within a group of closely related edible ectomycorrhizal Amanita from North America (the American Caesar's mushrooms species complex) using multilocus coalescent‐based approaches; and then address questions related to effects of Pleistocene climate change on the diversity and genetics of the group. Our study includes extensive geographical sampling throughout the distribution range, and DNA sequences from three nuclear protein‐coding genes. Results reveal cryptic diversity and high speciation rates in refugia. Population sizes and expansions seem to be larger at midrange latitudes (Mexican highlands and SE USA). Range shifts are proportional to population size expansions, which were overall more common during the Pleistocene. This study documents responses to past climate change in fungi and also highlights the applicability of the multispecies coalescent in comparative phylogeographical analyses and diversity assessments that include ancestral species.     

Phylogeography of a subterranean amphipod reveals cryptic diversity and dynamic evolution in extreme environments

Extreme conditions in subsurface are suspected to be responsible for morphological convergences, and so to bias biodiversity assessment. Subterranean organisms are also considered as having poor dispersal abilities that in turn generate a large number of endemic species when habitat is fragmented. Here we test these general hypotheses using the subterranean amphipod Niphargus virei. All our phylogenetic analyses (Bayesian, maximum likelihood and distance), based on two independent genes (28S and COI), revealed the same tripartite structure. N. virei populations from Benelux, Jura region and the rest of France appeared as independent evolutionary units. Molecular rates estimated via global or Bayesian relaxed clock suggest that this split is at least 13 million years old and accredit the cryptic diversity hypothesis. Moreover, the geographical distribution of these lineages showed some evidence of recent dispersal through apparent vicariant barrier. In consequence, we argue that future analyses of evolution and biogeography in subsurface, or more generally in extreme environments, should consider dispersal ability as an evolving trait and morphology as a potentially biased marker.