Diversity and ecology of soil fungal communities in rubber plantations

Monoculture rubber cultivation and its intensive associated human activities are known to have a negative impact on the biodiversity, ecology, and biological conservation of the ecosystems in which they occur. These negative impacts include changes to the biodiversity and function of soil fungal communities, which contribute towards nutrient cycling and interact with other organisms in belowground ecosystems, and may be pathogens. Despite the important role of soil fungi in rubber plantations, these communities have been poorly studied. In this paper, we review the existing literature on the diversity and ecology of belowground fungi in rubber plantations. Various groups of soil fungi, including saprobes, symbionts, and pathogens are discussed. Additionally, the role of plantation management is discussed in the context of both pathogenic soil fungi and the promotion of beneficial soil fungi. Management practices include clone selection, tree age and planting density, application of chemicals, and intercropping systems. Our review shows the strong need for further research into the effects of monoculture rubber plantations on soil fungal communities, and how we can best manage these systems in the future, in order to create a more sustainable approach to rubber production.     

Patterns of fungal diversity and composition along a salinity gradient

Estuarine salinity gradients are known to influence plant, bacterial and archaeal community structure. We sequenced 18S rRNA genes to investigate patterns in sediment fungal diversity (richness and evenness of taxa) and composition (taxonomic and phylogenetic) along an estuarine salinity gradient. We sampled three marshes—a salt, brackish and freshwater marsh—in Rhode Island. To compare the relative effect of the salinity gradient with that of plants, we sampled fungi in plots with Spartina patens and in plots from which plants were removed 2 years prior to sampling. The fungal sediment community was unique compared with previously sampled fungal communities; we detected more Ascomycota (78%), fewer Basidiomycota (6%) and more fungi from basal lineages (16%) (Chytridiomycota, Glomeromycota and four additional groups) than typically found in soil. Across marshes, fungal composition changed substantially, whereas fungal diversity differed only at the finest level of genetic resolution, and was highest in the intermediate, brackish marsh. In contrast, the presence of plants had a highly significant effect on fungal diversity at all levels of genetic resolution, but less of an effect on fungal composition. These results suggest that salinity (or other covarying parameters) selects for a distinctive fungal composition, and plants provide additional niches upon which taxa within these communities can specialize and coexist. Given the number of sequences from basal fungal lineages, the study also suggests that further sampling of estuarine sediments may help in understanding early fungal evolution.     

不同密度巨桉人工林林下植物多样性及根际土壤化感物质

为探究巨桉人工林林下植物多样性的影响因素,选择四川省丹棱县4和8年生不同密度(1200、1600和2000株·hm^-2)巨桉人工林为对象,研究林下植物多样性和根际土壤酚类化感物质。结果表明: 共发现植物45种,隶属于33科44属;随林龄增加和林分密度降低,巨桉人工林林下植物种类增加且重要值分布更为均匀;各林分植物生活型以高位芽植物为主。4年生林地灌木Shannon指数和Margalef指数在1600株·hm^-2下显著升高,4年生林地除Margalef指数外其余草本多样性指数及8年生林地草本Pielou指数随林分密度降低均显著升高;灌木Shannon指数及Margalef指数在1200株·hm^-2下8年生林地显著高于4年生林地。根际土壤中鉴定出5种酚类化感物质,4年生林地根际土壤中水杨酸浓度在1600株·hm^-2下显著降低,5,7-二羟基黄酮浓度随林分密度降低而显著降低;水杨酸浓度在8年生林地根际土壤中随林分密度降低显著升高;水杨酸浓度在2000株·hm^-2下4年生林地显著高于8年生林地,在1600株·hm^-2下相反;5,7-二羟基黄酮浓度在1200株·hm^-2下8年生林地显著高于4年生林地。冗余分析(RDA)结果表明,土壤pH、容重、有机质、全磷、全氮及化感物质是林下植物多样性的主要环境影响因子。适度延长轮伐期、调节林分密度以改善林内微环境、缓冲巨桉的化感作用,可促进林下植被发育。     

Changes in ectomycorrhizal fungal community composition and declining diversity along a 2‐million‐year soil chronosequence

Ectomycorrhizal (ECM) fungal communities covary with host plant communities along soil fertility gradients, yet it is unclear whether this reflects changes in host composition, fungal edaphic specialization or priority effects during fungal community establishment. We grew two co‐occurring ECM plant species (to control for host identity) in soils collected along a 2‐million‐year chronosequence representing a strong soil fertility gradient and used soil manipulations to disentangle the effects of edaphic properties from those due to fungal inoculum. Ectomycorrhizal fungal community composition changed and richness declined with increasing soil age; these changes were linked to pedogenesis‐driven shifts in edaphic properties, particularly pH and resin‐exchangeable and organic phosphorus. However, when differences in inoculum potential or soil abiotic properties among soil ages were removed while host identity was held constant, differences in ECM fungal communities and richness among chronosequence stages disappeared. Our results show that ECM fungal communities strongly vary during long‐term ecosystem development, even within the same hosts. However, these changes could not be attributed to short‐term fungal edaphic specialization or differences in fungal inoculum (i.e. density and composition) alone. Rather, they must reflect longer‐term ecosystem‐level feedback between soil, vegetation and ECM fungi during pedogenesis.     

Soil fungal diversity and assembly along a xeric stress gradient in the central Namib Desert

The Namib Desert of south-western Africa is one of the oldest deserts in the world and possesses unique geographical, biological and climatic features. While research through the last decade has generated a comprehensive survey of the prokaryotic communities in Namib Desert soils, little is yet known about the diversity and function of edaphic fungal communities, and even less of their responses to aridity. In this study, we have characterized soil fungal community diversity across the longitudinal xeric gradient across the Namib desert (for convenience, divided into the western fog zone, the central low-rainfall zone and the eastern high-rainfall zone), using internal transcribed sequence (ITS) metabarcoding. Ascomycota, Basidiomycota and Chytridiomycota consistently dominated the Namib Desert edaphic fungal communities and a core mycobiome composed of only 15 taxa, dominated by members of the class Dothideomycetes (Ascomycota), was identified. However, fungal community structures were significantly different in the fog, low-rainfall and high-rainfall zones. Furthermore, Namib Desert gravel plain fungal community assembly was driven by both deterministic and stochastic processes; the latter dominating in the all three xeric zones. We also present data that suggest that the inland limit of fog penetration represents an ecological barrier to fungal dispersal across the Namib Desert.     

纳帕海高原湿地真菌群落多样性和组成的分布

【背景】位于滇西北的纳帕海高原湿地,是我国唯一的低纬度、高海拔、季节性半封闭型高原湿地。真菌在湿地生态系统的维持和稳定中发挥着特殊作用,然而关于纳帕海高原湿地真菌群落多样性和组成的研究目前仍无报道。【目的】对纳帕海高原湿地不同季节和土壤类型真菌群落多样性和组成及与环境因子的关系开展系统研究分析,促进对高原湿地微生物多样性的深入认识。【方法】采用荧光定量PCR和高通量测序技术,分析了纳帕海高原湿地不同季节和土壤类型中真菌的数量、群落多样性和组成及其与环境因子的关系。【结果】真菌数量级的变化对于人为干扰下的湿地土壤退化是敏感的响应指标。在真菌群落组成中,约有60%以上未确定的分类信息,40%有确定分类信息的包括6个门17个纲37个目53个科63个属,大部分分类信息集中在Ascomycota门,相对优势属为Gibberella。通过分类水平、OTU水平和β多样性分析比较,在纳帕海高原湿地整体真菌群落多样性和组成受季节变化影响不显著,但不同土壤类型的变化呈显著差异,推测是由于不同采样区植物根际效应和种类的影响。CCA (Canonical correlation analysis)分析表明,在不同采样区受不同土壤理化因子的影响。【结论】揭示了纳帕海高原湿地土壤真菌群落多样性和组成的区域特征,从微生物学角度进一步提出了对纳帕海高原湿地环境保护和恢复的重要性。     

桂西北喀斯特地区不同退化程度植被群落物种组成及多样性特征

世界范围内,很多自然生态系统均在不同程度上受到了损害,喀斯特脆弱生态系统的退化是一个复合过程,喀斯特地区不同退化程度植被群落特征有何差异有待研究。该文采用样方法进行全面的调查,研究了桂西北喀斯特地区5个退化程度植被群落的物种组成、群落结构特征和物种多样性。结果表明:(1)不同退化程度群落物种组成和生活型组成有较大差异,潜在退化群落科属种丰富度最高,沿着退化程度递增的梯度,群落乔木树种逐渐减少至消失,灌木比例呈先增后减的趋势,草本比例逐渐增加。(2)调查到维管束植物218种,隶属于86科168属;以大戟科、楝科、蔷薇科、马鞭草科、禾本科和肾蕨科植物为主;退化过程中,优势种的重要值逐渐降低,其在群落内的支配地位逐渐减弱,伴生种重要值逐渐升高。(3)退化过程中,群落结构趋于简单化,群落木本植物密度、高度和盖度逐渐减少。(4)不同退化程度植被群落乔灌草层物种多样性存在显著性差异,随着退化程度的增加,群落总植被物种丰富度指数、Shannon-Wiener多样性指数、Simpson优势度指数整体呈下降趋势。     

Changes in fungal community of Scots pine (Pinus sylvestris) needles along a latitudinal gradient in Sweden

Conifer needles are typically long lived and can host a diverse community of fungal species with various effects on their host tree. The purpose of this study was to analyse shifts in the fungal community of Scots pine (Pinus sylvestris) needles on different spatial scales using 454 pyrosequencing. The fungal community composition changed gradually along a north-south gradient through Sweden, representing boreal to temperate vegetation zones. OTU richness and Shannon's diversity index increased with increasing latitude, but only in naturally regenerated forests. On the tree level, needles with symptoms of disease hosted a more diverse mycobiota compared to healthy needles, presumably supporting more pathogenic or saprotrophic species. This study provides a better insight into the patterns of fungal communities of Scots pine needles and highlights the need for further experimental research to identify specific environmental factors shaping the abundance of different fungal species.     

Influence of soil nutrients on ectomycorrhizal communities in a chronosequence of mixed temperate forests

Many factors associated with forests are collectively responsible for controlling ectomycorrhizal (ECM) fungal community structure, including plant species composition, forest structure, stand age, and soil nutrients. The objective of this study was to examine relationships among ECM fungal community measures, local soil nutrients, and stand age along a chronosequence of mixed forest stands that were similar in vegetation composition and site quality. Six combinations of age class (5-, 26-, 65-, and 100-year-old) and stand initiation type (wildfire and clearcut) were replicated on four sites, each representing critical seral stages of stand development in Interior Cedar-Hemlock (ICH) forests of southern British Columbia. We found significant relationships between ECM fungal diversity and both available and organic P; available P was also positively correlated with the abundance of two ECM taxa (Rhizopogon vinicolor group and Cenoccocum geophilum). By contrast, ECM fungal diversity varied unpredictably with total and mineralizable N or C to N ratio. We also found that soil C, N, available P, and forest floor depth did not exhibit strong patterns across stand ages. Overall, ECM fungal community structure was more strongly influenced by stand age than specific soil nutrients, but better correlations with soil nutrients may occur at broader spatial scales covering a wider range of site qualities.     

Pine species determine fungal microbiome composition in a common garden experiment

The factors shaping the composition of microbial communities in trees remain poorly understood. We evaluated whether the core and satellite fungal communities in five pine species (Pinus radiata, Pinus pinaster, Pinus sylvestris, Pinus nigra, and Pinus uncinata) were shaped by the host species identity. Because the trees had earlier been inoculated with a fungal pathogen (Fusarium circinatum), we also explored the possibilities to detect its presence and potential co-occurrence networks. We found interspecific variation in the fungal community composition and abundance among the different tree species and the existence of a core microbiome that was independent of the host species. The presence of F. circinatum was confirmed in some samples through qPCR but the pathogen did not co-occur with a specific fungal community. The results highlight the importance of host species as a determinant of microbiome assembly in common environments.     

Changes in arbuscular mycorrhizal fungal communities along a river delta island in northeastern Brazil

Arbuscular mycorrhizal fungi (AMF) play a key role in the maintenance of the balance of terrestrial ecosystems, but little is known about the biogeography of these fungi, especially on tropical islands. This study aims to compare AMF community structure along a transect crossing a fluvial-marine island and relate these communities with soil and vegetation parameters to shed light on the forces driving AMF community structure on a local scale. We tested the hypothesis that the composition of AMF communities changes across the island, even within short distances among sites, in response to differences in edaphic characteristics and vegetation physiognomies. We sampled roots and soils in five different natural and degraded habitats: preserved mangrove forest (MF), degraded mangrove forest (MD), natural Restinga forest (RF), and two regeneration Restinga forests (RR1 and RR2) on Ilha da Restinga, northeastern Brazil. We determined the mycorrhizal colonization rate and AMF community structure based on morphological spore identification. The island soils were sandy with pH varying from acid to neutral; higher levels of organic matter were registered in RF and lower in MF; other chemical and physical soil attributes differed along the habitat types on the island. In total, 22 AMF species were identified, without any difference in species richness. However, the diversity and composition of AMF communities, spore abundance per families, and mycorrhizal colonization were statistically different among the habitats. The composition of AMF communities was strongly related to soil characteristics, especially the sum of exchangeable bases. Our results indicate that the different habitat types have diverse AMF communities even within short distances among habitats. In conclusion, islands with high spatial heterogeneity in soil parameters and diverse vegetation are potential refuges for the diversity conservation of AM fungi.     

Soil CO<Subscript>2</Subscript> efflux in loblolly pine (<Emphasis Type="Italic">Pinus taeda</Emphasis> L.) plantations on the Virginia Piedmont and South Carolina Coastal Plain over a rotation-length chronosequence

We measured soil surface CO₂ efflux (F_s) in loblolly pine stands (Pinus taeda L.) located on the Virginia Piedmont (VA) and South Carolina Coastal Plain (SC) in efforts to assess the impact climate, productivity, and cultural practices have on F_s in the managed loblolly pine ecosystem. The effect of stand age on F_s was examined using a replicated chronosequence approach in which stands ranging from 1 to 25 years since planting were investigated. Soil CO₂ efflux was measured on both VA and SC sites for over a year using a closed dynamic system. Multiple linear regression was used to evaluate F_s correlates and examine the relationship between candidate explanatory variables and F_s. Soil temperature (top 10 cm) was the major correlate with F_s on both locations. We observed a positive age effect on F_s in VA stands and no relationship between age and F_s in SC stands. Annual soil C efflux declined with stand age in SC due to both reductions in soil temperatures as crown closure occurs and a diminishing heterotrophic C substrate pool. Annual estimated efflux ranges from 16.7 to 13.2 Mg C ha⁻¹ for 1 and 20-year-old stands, respectively. In contrast, annual soil C efflux increased with age in VA stands as a result of the positive relationship between stand age and F_s, which appears to be related to an increase in the contribution of root respiration to total F_s over time. In VA stands, efflux estimates range from 7.6 to 12.3 Mg C ha⁻¹ for 1 and 20-year-old stands, respectively. These results demonstrate the need to further consider the impact forest management and within-region variability have on soil C efflux over time when estimating C budgets.     

不同坡位下巨桉人工林土壤动物群落特征

为了解坡位对巨桉人工林土壤动物群落结构的影响,2009年1-10月,调查了四川盆地低山丘陵区不同坡位巨桉人工林的土壤动物群落.从3个巨桉人工林共获取土壤动物34741只,鉴定出146个类群,隶属于7门16纲31目;巨桉人工林下土壤动物的群落组成、营养类群、多样性及其季节动态基本都存在坡位变化,大型和中小型干生土壤动物的个体数、大型土壤动物的腐食性类群和中小型干生土壤动物的杂食性类群数量表现出随坡位的下降而逐渐增多的趋势,说明土壤动物响应了坡位引起的土壤生态因子的变化.其中大型土壤动物的腐食性类群和中小型湿生土壤动物的多样性显示出显著的坡位差异,表明这两个指标能指示巨桉人工林不同坡位生境的异质性.总的看来,巨桉人工林坡位因子对土壤动物群落的分布及结构特征具有一定影响,但作用尚不显著.     

Responses of litter decomposition to temperature along a chronosequence of tropical montane rainforest in a microcosm experiment

We conducted a microcosm experiment for studying the decomposition of Altingia obovata leaf litter by the decomposer community at 20 and 30°C from three forest stands (namely a 35-year-old secondary forest, a 47-year-old secondary forest, and a primary forest) of a tropical montane rainforest. Our results showed that rank-order of the litter decomposition among the three forest stands was not parallel to the stand age. At 20°C, the mass loss of A. obovata leaf litter from the primary forest was higher than those from the two secondary forests, of which the younger stand showed higher mass loss than did the older one. However, there were no differences in mass loss among these three stands at 30°C. The mass loss for the two secondary forest stands, but not for the primary forest stand, increased significantly from 20 to 30°C. The level of lignin decomposition among the three stands at 20°C corresponded to their forest stand age, i.e., the primary forest > the 47-year-old secondary forest > the 35-year-old secondary forest. A rise of 10°C in temperature significantly increased lignin decomposition for the two secondary forests, while the reverse was true for the primary forest. Carbohydrate decomposition was positively related to the temperature but not to the stand age. The different responses of litter decomposition to the forest stand age and temperature might be due to the differences in the microbial activities among the three forest stands.     

Effect of tree host species on fungal community composition in a tropical rain forest in Panama

Abstract.  To determine whether host species influence the composition of fungal communities, the ascomycetes and basidiomycetes present on three tree species ( Prioria copaifera (Fabaceae), Quararibea asterolepis (Bombacaceae), and Trichilia tuberculata (Meliaceae)) were sampled on the 50-ha Forest Dynamics Project plot in lowland moist tropical forest on Barro Colorado Island, Panama. The most abundant fungal morphotypes of both ascomycetes and basidiomycetes were generalists found on all three hosts, but detrended correspondence analysis revealed distinct differences in fungal community composition among host trees. These differences among hosts were constant across census years. Randomization tests revealed that there were significantly fewer host-generalist fungi than expected for ascomycetes but not for basidiomycetes. These results indicate that host composition plays a role in structuring both ascomycete and basidiomycete fungal communities, but that the most successful fungal morphotypes are capable of colonizing multiple host species.     

一个年龄序列巨桉人工林植物和土壤生物多样性

为了全面、系统研究和评价退耕后桉树人工林生物多样性,采用立地条件控制及空间代替时间法,对四川丹棱县退耕营造的巨桉(Eucalyptus grands)人工林(1-10a)植物和土壤生物多样性进行了同步研究.结果显示,植物和土壤动物的物种数、密度和多样性指数及土壤微生物数量呈相似变化趋势,即轮伐期前同步(4a左右)降低,此后随林龄显著增加.CCA分析显示,植物生活型随林龄由藤本植物、地面芽和1年生植物向多年生草本高位芽和高位芽植物过渡.土壤微生物以细菌占据数量优势;土壤动物以腐食性功能团占据优势,杂食性次之.腐食性功能团1-7a降低而后升高,杂食性呈S型升高趋势;植食性和捕食性功能团百分比较低随林龄显著降低.土壤动物优势类群中线虫纲个体百分比随林龄显著降低,蜱螨目百分比和A/C值(蜱螨目/弹尾目数量比)呈S型上升趋势.各林龄巨桉林地植物多样性均显著高于对照农耕地;除1,2a及4-7a样地植物多样性显著低于对照马尾松林,其余均与其无显著差异.土壤生物多样性,轮伐期前巨桉林地与对照农耕地差异不显著,此后则显著高于农耕地;各林龄样地土壤生物多样性均显著低于对照马尾松林.植物和土壤生物多样性指标显著相关,且相关系数随土壤层次加深而降低.     

典型农田退耕后土壤真菌与细菌群落的演替

土壤真菌和细菌作为地下生态系统的重要组成部分,其群落的恢复状况是评价农田退耕还林生态效益的重要指标。以云南省维西县典型退耕还林农田为对象,利用高通量测序等方法比较了不同退耕年限的农田土壤中真菌和细菌群落随植被演替的变化特征。结果发现,农田撂荒后土壤细菌多样性先显著降低后缓慢上升,真菌多样性变化不明显;地上部植被由草本经灌丛再向林地演替的过程中,土壤真菌的群落组成随植被变化呈现明显的改变,主要体现在粪壳菌纲(Sordariomycetes)所占比例的减少(由30%减至10%左右)和伞菌纲(Agaricomycetes)所占比例的增加(由5%以下增至20%以上);而细菌的群落组成无明显变化。聚类分析的结果显示,真菌的群落组成变化与植物群落的演替规律更为同步。不同演替阶段的退耕农田土壤真菌和细菌群落均明显区别于未经扰动的天然林,表明人为扰动对土壤微生物群落的影响可能在较长时间内持续存在。研究揭示了云南典型农田退耕后地下土壤真菌和细菌群落随植被演替的变化特征,为全面评价该地区退耕还林的生态效益提供了数据支撑。     

Successional dynamics of soil fungal diversity along a restoration chronosequence post‐coal mining

Soil disruption from open‐cut mining practices can adversely impact microbial communities and the ecosystem services that they mediate. Despite this, assessment of impacts of soil disruption, and the subsequent recovery of microbial communities is rarely studied. Monitoring of ecological restoration success on mine sites has traditionally focused on vegetation; however, most plants rely, at least in part, on associations with soil fungi for enhanced nutrient and water acquisition. Here, we used high‐throughput phylogenetic marker gene sequencing to characterize the diversity of soil fungal communities along a restoration chronosequence ranging from 3 to 23 years at a rehabilitated mine site. We used nonmined analogue sites as a baseline for comparative purposes and examined the associations of soil fungal communities with soil physicochemical and aboveground vegetation variables. Fungal richness on rehabilitated sites was significantly larger than on nonmined sites, suggesting that mixing of topsoil during stockpiling resulted in a composite microbial community. Fungal community composition was significantly influenced by edaphic variables and the length of rehabilitation, with mined sites becoming more similar to nonmined sites over time. Fungal populations associated with ectomycorrhizae were relatively more abundant than those associated with arbuscular mycorrhizae and declined in response to disturbance, but recovered over time on the woody dominated sites indicating a strong coupling of these fungi with aboveground vegetation. Our data indicate that soil fungal diversity is a useful bioindicator of soil restoration in mined sites and may complement more traditional vegetation‐based surveys.     

Ericoid mycorrhizal colonization and associated fungal communities along a wetland gradient in the Acadian forest of Eastern Canada

Wetlands provide numerous ecosystem services, and ericaceous plants are important components of these habitats. However, the ecology of fungi associated with ericaceous roots in these habitats is poorly known. To investigate fungi associated with ericaceous roots in wetlands, ericoid mycorrhizal colonization was quantified, and fungal communities were characterized on the roots of Gaultheria hispidula and Kalmia angustifolia along two upland – forested wetland transects in spring and fall. Ericoid mycorrhizal colonization was significantly higher in the wetlands for both plant species. Both upland and wetland habitats supported distinct assemblages of ericaceous root associated fungi including habitat specific members of the genus Serendipita. Habitat was a stronger driver of ericoid mycorrhizal colonization and ericaceous root associated community composition than host or sampling season, with differences related to soil water content, soil nutrient content, or both. Our results indicate that ericaceous plant roots in forested wetlands are heavily colonized by habitat specific symbionts.     

Long-term impact of pulses crop rotation on soil fungal diversity in aerobic and wetland rice cultivation

Pulse crop rotation in rice cultivation is a widely accepted agronomic practice. Depending upon the water regime, rice cultivation has been classified into wetland and aerobic practices. However, no studies have been conducted so far to understand the impact of pulse crop rotation and rice mono-cropping on fungal diversity, particularly in aerobic soil. A targeted metagenomic study was conducted to compare the effects of crop rotations (rice-rice and rice-pulse) on fungal diversity in wetland and aerobic rice soils. Out of 445 OTUs, 41.80% was unknown and 58.20% were assigned to six phyla, namely Ascomycota (56.57%), Basidiomycota (1.32%), Zygomycota (0.22%), Chytridiomycota (0.04%), Glomeromycota (0.03%), and Blastocladiomycota (0.02%). Functional trait analysis found wetland rice-pulse rotation increased symbiotrophs (36.7%) and saprotrophs (62.1%) population, whereas higher pathotrophs were found in aerobic rice–rice (62.8%) and rice-pulse (61.4%) cropping system. Certain soil nutrients played a major role in shaping the fungal community; Ca had significant (p < 0.05) positive impact on saprotroph, symbiotroph and endophytes, whereas Cu had significant (p < 0.05) negative impact on pathotrophs. This study showed that rice-pulse crop rotation could enhance the saprophytic and symbiotic fungal diversity in wetland and reduce the population of pathogens in aerobic rice cultivation.