基于高通量测序的褐飞虱肠道微生物多样性分析

【目的】探明褐飞虱Nilaparvata lugens成虫肠道微生物群落结构和多样性。【方法】分离褐飞虱成虫完整肠道并提取总DNA,利用Illumina MiSeq(PE300)技术对其肠道细菌16S rRNA的V3-V4变异区和真菌ITS2序列进行测序,统计肠道微生物的操作分类单元(operational taxonomic unit, OTU)数量,分析其物种组成、丰度及Alpha多样性。并通过qPCR技术验证随机挑选注释到的4种肠道菌的高通量测序数据的有效性。【结果】分别获得褐飞虱成虫肠道细菌16S rRNA和真菌ITS2优质序列32 395和24 986条,根据序列相似性进行聚类分析分别获得235和128个OTUs。其中,细菌共注释到7个门, 15个纲, 26个目, 45个科和73个属;真菌共鉴定到3个门, 9个纲, 12个目, 15个科和18个属。在门分类水平上,细菌以变形菌门(Proteobacteria)、拟杆菌门(Bacteroidetes)和厚壁菌门(Firmicutes)为优势门类;真菌以子囊菌门(Ascomycota)为绝对优势菌门。在属分类水平上,细菌的优势属为不动杆菌属Acinetobacter以及紫单胞菌科(Porphyromonadaceae)未确定属和毛螺菌科(Lachnospiraceae)未确定属,其丰度分别为36.37%, 17.22%和15.01%;真菌的优势属为粪壳菌纲(Sordariomycetes)未确定属,丰度为95.77%。Alpha多样性分析结果显示,褐飞虱肠道细菌(真菌)的观测物种数、Chao1指数、Shannon指数和Simpson 指数分别为235(128), 262.64(165.40), 3.90(0.91)和0.62(0.75)。4种肠道菌的qPCR结果显示高通量测序数据具有较高的有效性。【结论】褐飞虱成虫肠道细菌和真菌群落整体多样性比较丰富。研究结果为从共生微生物角度解析褐飞虱的环境适应性以及开发基于微生物防治的新技术等方面提供了依据。     

毛木耳不同生长期菌棒微生物群落研究

为探究毛木耳(Auricularia cornea)代料栽培子实体不同生育阶段菌棒内细菌和真菌群落，基于Illumina Miseq测序平台，对毛木耳4个出耳期(ful、pri、ope和mat)菌棒的微生物群落进行分析。获得细菌16S rRNA有效序列503 724条，真菌ITS有效序列712 728条。细菌物种注释分属25门54纲85目134科199属；真菌物种注释隶属5门9纲15目12科19属。菌棒中有非常丰富的细菌群落，主要分属于变形菌门(Proteobacteria)、厚壁菌门(Firmicutes)、放线菌门(Actinobacteria)和拟杆菌门(Bacteroidetes)。相对丰度最高的前2个属：ful期是Lysinibacillus(25.71%)和Acinetobacter(14.38%);pri期是Pseudomonas(35.85%)和Solibacillus(14.85%);ope期是Lysinibacillus(36.42%)和Pseudomonas(21.73%);mat期是Acinetobacter(27.94%)和Ochrobactrum(14.92...     

Changes in Root Bacterial Communities Associated to Two Different Development Stages of Canola (Brassica napus L. var oleifera) Evaluated through Next-Generation Sequencing Technology

Crop production may benefit from plant growth-promoting bacteria. The knowledge on bacterial communities is indispensable in agricultural systems that intend to apply beneficial bacteria to improve plant health and production of crops such as canola. In this work, the diversity of root bacterial communities associated to two different developmental phases of canola (Brassica napus L.) plants was assessed through the application of new generation sequencing technology. Total bacterial DNA was extracted from root samples from two different growth states of canola (rosette and flowering). It could be shown how bacterial communities inside the roots changed with the growing stage of the canola plants. There were differences in the abundance of the genera, family, and even the phyla identified for each sample. While in both root samples Proteobacteria was the most common phylum, at the rosette stage, the most common bacteria belonged to the family Pseudomonadaceae and the genus Pseudomonas, and in the flowering stage, the Xanthomonadaceae family and the genus Xanthomonas dominated the community. This implies in a switch in the predominant bacteria in the different developmental stages of the plant, suggesting that the plant itself interferes with the associated microbial community.     

不同生境黑果枸杞根际与非根际土壤微生物群落多样性

研究典型生境黑果枸杞根际与非根际土壤微生物群落多样性及其与土壤理化性质间的关系,为进一步研究黑果枸杞抗逆性提供理论数据。采集新疆精河县艾比湖地区(EB)盐碱地、乌苏市(WS)路旁荒地、五家渠市(WQ)人工林带的黑果枸杞根际与非根际土壤,利用Illumina-MiSeq高通量测序技术分析细菌和真菌群落组成和多样性。结果表明:根际土壤细菌多样性高于非根际土壤(WQ除外),而根际真菌多样性低于非根际土壤。WQ非根际土壤细菌和真菌多样性均高于EB和WS;根际细菌多样性排序为EBWSWQ,根际真菌多样性排序为WSEBWQ。根际土壤优势细菌门依次是变形菌门、拟杆菌门、放线菌门、酸杆菌门,真菌优势门为子囊菌门、担子菌门。根际土壤细菌变形菌门、拟杆菌门、酸杆菌门的相对丰度高于非根际土壤,而厚壁菌在根际土壤中的丰度显著降低,真菌优势门丰度在根际土和非根际土中的变化趋势因地区而异; Haliea、Gp10、Pelagibius、Microbulbifer、假单胞菌属、Thioprofundum、Deferrisoma是根际土壤细菌优势属;多孢子菌属、支顶孢属、Corollospora、Cochlonema是根际真菌优势属。细菌、真菌优势类群(门、属)的组成以及丰富度存在地区间差异,厚壁菌门在EB地区的丰富度显著高于含盐量较低的WS、WQ;盐碱生境EB中根际土壤嗜盐细菌的丰度高于非盐碱生境(WQ、WS),如盐单胞菌属、动性球菌属、Geminicoccu、Pelagibius、Gracilimonas、Salinimicrobium等。小囊菌属是EB根际真菌的最优势属,Melanoleuca是WQ和WS的最优势属,地孔菌属、Xenobotrytis、Brachyconidiellopsis、多孢子菌属等在EB根际土壤中的丰度显著高于WQ和WS。非盐碱生境(WS和WQ)的微生物群落之间的相似性较高,并且高于与盐碱环境(EB)之间的相似性,表明土壤含盐量对微生物群落组成丰度具有重要的影响。     

Inhibitory bacteria reduce fungi on early life stages of endangered Colorado boreal toads (Anaxyrus boreas)

Increasingly, host-associated microbiota are recognized to mediate pathogen establishment, providing new ecological perspectives on health and disease. Amphibian skin-associated microbiota interact with the fungal pathogen, Batrachochytrium dendrobatidis (Bd), but little is known about microbial turnover during host development and associations with host immune function. We surveyed skin microbiota of Colorado''s endangered boreal toads (Anaxyrus boreas), sampling 181 toads across four life stages (tadpoles, metamorphs, subadults and adults). Our goals were to (1) understand variation in microbial community structure among individuals and sites, (2) characterize shifts in communities during development and (3) examine the prevalence and abundance of known Bd-inhibitory bacteria. We used high-throughput 16S and 18S rRNA gene sequencing (Illumina MiSeq) to characterize bacteria and microeukaryotes, respectively. Life stage had the largest effect on the toad skin microbial community, and site and Bd presence also contributed. Proteobacteria dominated tadpole microbial communities, but were later replaced by Actinobacteria. Microeukaryotes on tadpoles were dominated by the classes Alveolata and Stramenopiles, while fungal groups replaced these groups after metamorphosis. Using a novel database of Bd-inhibitory bacteria, we found fewer Bd-inhibitory bacteria in post-metamorphic stages correlated with increased skin fungi, suggesting that bacteria have a strong role in early developmental stages and reduce skin-associated fungi.     

Microbiome changes through ontogeny of a tick pathogen vector

Blacklegged ticks (Ixodes scapularis) are one of the most important pathogen vectors in the United States, responsible for transmitting Lyme disease and other tick‐borne diseases. The structure of a host's microbial community has the potential to affect the ecology and evolution of the host. We employed high‐throughput sequencing of the 16S rRNA gene V3‐V4 hypervariable regions in the first study to investigate the tick microbiome across all developmental stages (larvae, nymphs, adults). In addition to field‐collected life stages, newly hatched laboratory‐reared larvae were studied to determine the baseline microbial community structure and to assess transovarial transmission. We also targeted midguts and salivary glands due to their importance in pathogen maintenance and transmission. Over 100 000 sequences were produced per life stage replicate. Rickettsia was the most abundant bacterial genus across all sample types matching mostly the Ixodes rickettsial endosymbionts, and its proportion decreased as developmental stage progressed, with the exception of adult females that harboured a mean relative abundance of 97.9%. Laboratory‐reared larvae displayed the lowest bacterial diversity, containing almost exclusively Rickettsia. Many of the remaining bacteria included genera associated with soil, water and plants, suggesting environmental acquisition while off‐host. Female organs exhibited significantly different β‐diversity than the whole tick from which they were derived. Our results demonstrate clear differences in both α‐ and β‐diversity among tick developmental stages and between tick organs and the tick as a whole. Furthermore, field‐acquired bacteria appear to be very important to the overall internal bacterial community of this tick species, with influence from the host bloodmeal appearing limited.     

Phylogenetic distribution of symbiotic bacteria from Panamanian amphibians that inhibit growth of the lethal fungal pathogen Batrachochytrium dendrobatidis

The introduction of next‐generation sequencing has allowed for greater understanding of community composition of symbiotic microbial communities. However, determining the function of individual members of these microbial communities still largely relies on culture‐based methods. Here, we present results on the phylogenetic distribution of a defensive functional trait of cultured symbiotic bacteria associated with amphibians. Amphibians are host to a diverse community of cutaneous bacteria and some of these bacteria protect their host from the lethal fungal pathogen Batrachochytrium dendrobatidis (Bd) by secreting antifungal metabolites. We cultured over 450 bacterial isolates from the skins of Panamanian amphibian species and tested their interactions with Bd using an in vitro challenge assay. For a subset of isolates, we also completed coculture experiments and found that culturing isolates with Bd had no effect on inhibitory properties of the bacteria, but it significantly decreased metabolite secretion. In challenge assays, approximately 75% of the bacterial isolates inhibited Bd to some extent and these inhibitory isolates were widely distributed among all bacterial phyla. Although there was no clear phylogenetic signal of inhibition, three genera, Stenotrophomonas, Aeromonas and Pseudomonas, had a high proportion of inhibitory isolates (100%, 77% and 73%, respectively). Overall, our results demonstrate that antifungal properties are phylogenetically widespread in symbiotic microbial communities of Panamanian amphibians and that some functional redundancy for fungal inhibition occurs in these communities. We hope that these findings contribute to the discovery and development of probiotics for amphibians that can mitigate the threat of chytridiomycosis.     

Stage correlation of symbiotic bacterial community and function in the development of litchi bugs (Hemiptera: Tessaratomidae)

Bacterial symbionts of insects have been shown to play important roles in host fitness. However, little is known about the bacterial community of Tessaratoma papillosa which is one of the most destructive pests of the well-known fruits Litchi chinensis Sonn and Dimocarpus longan Lour in Oriental Region, especially in South-east Asia and adjacent areas. In this study, we surveyed the bacterial community diversity and dynamics of T. papillosa in all developmental stages with both culture-dependent and culture-independent methods by the third-generation sequencing technology. Five bacterial phyla were identified in seven developmental stages of T. papillosa. Proteobacteria was the dominant phylum and Pantoea was the dominant genus of T. papillosa. The results of alpha and beta diversity analyses showed that egg stage had the most complex bacterial community. Some of different developmental stages showed similarities, which were clustered into three phases: (1) egg stage, (2) early nymph stages (instars 1–3), and (3) late nymph stages (instars 4–5) and adult stage. Functional prediction indicated that the bacterial community played different roles in these three phases. Furthermore, 109 different bacterial strains were isolated and identified from various developmental stages. This study revealed the relationship between the symbiotic bacteria and the development of T. papillosa, and may thus contribute to the biological control techniques of T. papillosa in the future.

     

不同树叶凋落物对人参土壤理化性质及微生物群落结构的影响

树种选择是林下山参护育成败的关键,研究树叶凋落物对人参土壤养分、微生物群落结构组成的影响,旨在为林下山参护育选择适宜林地及农田栽参土壤改良提供科学依据和理论指导。通过盆栽试验,研究添加5.0 g色木槭Acer mono.Maxim.var.mono(A)、赤松Pinus densiflora Sieb.et Zucc.(B)、胡桃楸Juglans mandshurica Maxim.(C)、紫椴Tilia amurensis Rupr.(D)、蒙古栎Quercus mongolica Fisch.ex Ledeb.(E)树叶凋落物到土壤中,种植人参(Panax ginseng C.A.meyer)后研究土壤理化性质以及微生物群落结构的变化。结果表明:添加不同树叶处理后人参土壤性质发生改变,土壤p H值显著高于对照土壤5.91(P0.05),土壤全氮、速效氮磷、微生物碳氮在所有树叶处理中显著增加(P0.05),而土壤容重、速效钾和C/N在添加树叶处理中降低。18个土壤样品基因组,经16S和ITS1测序分别得到6064和1900个OUTs。其中细菌涵盖了42门、117纲、170目、213科、225属,真菌涵盖了24门、98纲、196目、330科、435属。不同树叶处理人参土壤细菌和真菌地位发生改变,细菌Proteobacteria是树叶分解的关键微生物,添加树叶后其多样性显著高于对照(P0.05)。而细菌Bacteroidetes和真菌Basidiomycota可能是区别阔叶林和针叶林树种的关键微生物,针叶林中含量显著低于阔叶林(P0.05),而真菌Ascomycota是针叶林分解的关键微生物。进一步从不同分类水平上得到特定树叶凋落物的特异细菌和真菌。典型相关分析(CDA)表明细菌Bacteroidetes、Chloroflexi、Actinobacteria及真菌Basidiomycota、Zygomycota、Chytridiomycota及Ascomycota的位置及多样性的改变均与土壤因子SMBN、TN、AP、SOC、AK、C/N、p H有关。综上所述,添加不同树叶后不仅提高土壤微生物量碳氮、改善土壤理化性质,同时改变微生物群落结构组成,不同树叶处理土壤理化性质不同导致人参土壤微生物组成的差异,本结果对于林下参选地和农田栽参土壤微生物改良具有理论指导作用。     

阿尔泰银莲花根际土壤微生物多样性研究

为了解野生和栽培阿尔泰银莲花根际土壤微生物多样性的差异,该研究采用Illumina MiSeq高通量测序技术对野生和栽培阿尔泰银莲花根际土壤微生物的群落组成和多样性进行探究。结果表明:(1)野生阿尔泰银莲花根际土壤的真菌多样性显著高于栽培阿尔泰银莲花(P<0.05),而细菌多样性差异不显著(P>0.05); NMDS分析结果显示,野生和栽培阿尔泰银莲花根际土壤真菌群落结构差异更显著。(2)细菌9 566个可操作分类单元(OTUs)涉及39门127纲315目500科886属,真菌2 670个OTUs涉及15门57纲138目293科597属。在门水平上,细菌群落中的变形菌门、酸杆菌门、放线菌门及真菌群落中的担子菌门、子囊菌门、被孢霉门均为野生和栽培阿尔泰银莲花根际土壤优势菌门,但其相对丰度在不同生长方式下存在差异。(3)环境因子关联分析(RDA)结果显示,土壤有机质是影响土壤细菌群落的主要因子(P<0.05),土壤pH、碱解氮和有效磷是影响真菌群落的主要因子(P<0.05)。综上认为,野生和栽培下的阿尔泰银莲花根际土壤微生物群落组成和多样性存在显著差异,这种差异可能与不同生长条件下的土壤理化性质存在密切的联系,该研究结果对阿尔泰银莲花科学种植以及土壤改良具有一定意义。     

Microbial Community Assembly and Succession on Lake Sturgeon Egg Surfaces as a Function of Simulated Spawning Stream Flow Rate

We investigated microbial succession on lake sturgeon (Acipenser fulvescens) egg surfaces over the course of their incubation period as a function of simulated stream flow rate. The primary objective was to characterize the microbial community assembly during succession and to examine how simulated stream flow rate affect the successional process. Sturgeon eggs were reared under three flow regimes; high (0.55 m/s), low (0.18 m/s), and variable (0.35 and 0.11 m/s alternating 12 h intervals). Eggs were collected from each flow regime at different egg developmental stages. Microbial community DNA was extracted from egg surface and the communities were examined using 16S rRNA gene-based terminal restriction fragment length polymorphism and 454 pyrosequencing. Analysis of these datasets using principal component analysis revealed that microbial communities were clustered by egg developmental stages (early, middle, and late) regardless of flow regimes. 454 pyrosequencing data suggested that 90–98 % of the microbial communities were composed of the phyla Proteobacteria and Bacteroidetes throughout succession. β-Protebacteria was more dominant in the early stage, Bacteroidetes became more dominant in the middle stage, and α-Proteobacteria became dominant in the late stage. A total of 360 genera and 5,826 OTUs at 97 % similarity cutoff were associated with the eggs. Midway through egg development, the egg-associated communities of the low flow regime had a higher diversity than those communities developed under high or variable flow regimes. Results show that microbial community turnover occurred during embryogenesis, and stream flow rate influenced the microbial succession processes on the sturgeon egg surfaces.     

Chinese white truffles shape the ectomycorrhizal microbial communities of Corylus avellana

Here, we investigated the influence of Chinese white truffle (Tuber panzhihuanense) symbioses on the microbial communities associated with Corylus avellana during the early development stage of symbiosis. The microbial communities associated with ectomycorrhizae, and associated with roots without T. panzhihuanense colonization, were determined via high-throughput sequencing of bacterial 16S rRNA genes and fungal ITS genes. Microbial community diversity was higher in the communities associated with the ectomycorrhizae than in the control treatment. Further, bacterial and fungal community structures were different in samples containing T. panzhihuanense in association with C. avellana compared to the control samples. In particular, the bacterial genera Rhizobium, Pedomicrobium, and Herbiconiux were more abundant in the ectomycorrhizae, in addition to the fungal genus Monographella. Moreover, there were clear differences in some physicochemical properties among the rhizosphere soils of the two treatments. Statistical analyses indicated that soil properties including exchangeable magnesium and exchangeable calcium prominently influenced microbial community structure. Lastly, inference of bacterial metabolic functions indicated that sugar and protein metabolism functions were significantly more enriched in the communities associated with the ectomycorrhizae from C. avellana mycorrhized with T. panzhihuanense compared to communities from roots of cultivated C. avellana without T. panzhihuanense. Taken together, these results highlight the interactions among ectomycorrhizal fungi, soil properties, and microbial communities that are associated with host plants and further our understanding of the ecology and cultivation of the economically important T. panzhihuanense truffles.

     

Arbuscular mycorrhizal fungal community divergence within a common host plant in two different soils in a subarctic Aeolian sand area

There is rising awareness that different arbuscular mycorrhizal (AM) fungi have different autoecology and occupy different soil niches and that the benefits they provide to the host plant are dependent on plant-AM fungus combination. However, the role and community composition of AM fungi in succession are not well known and the northern latitudes remain poorly investigated ecosystems. We studied AM fungal communities in the roots of the grass Deschampsia flexuosa in two different, closely located, successional stages in a northern Aeolian sand area. The AM fungal taxa richness in planta was estimated by cloning and sequencing small subunit ribosomal RNA genes. AM colonization, shoot δ ¹³C signature, and %N and %C were measured. Soil microbial community structure and AM fungal mycelium abundance were estimated using phospholipid (PLFA) and neutral lipid (NLFA) analyses. The two successional stages were characterized by distinct plant, microbial, and fungal communities. AM fungal species richness was very low in both the early and late successional stages. AM frequency in D. flexuosa roots was higher in the early successional stage than in the late one. The AM fungal taxa retrieved belonged to the genera generally adapted to Arctic or extreme environments. AM fungi seemed to be important in the early stage of the succession, suggesting that AM fungi may help plants to better cope with the harsh environmental conditions, especially in an early successional stage with more extreme environmental fluctuations.     

The roles of host evolutionary relationships (genus: Nasonia) and development in structuring microbial communities

The comparative structure of bacterial communities among closely related host species remains relatively unexplored. For instance, as speciation events progress from incipient to complete stages, does divergence in the composition of the species’ microbial communities parallel the divergence of host nuclear genes? To address this question, we used the recently diverged species of the parasitoid wasp genus Nasonia to test whether the evolutionary relationships of their bacterial microbiotas recapitulate the Nasonia phylogenetic history. We also assessed microbial diversity in Nasonia at different stages of development to determine the role that host age plays in microbiota structure. The results indicate that all three species of Nasonia share simple larval microbiotas dominated by the γ‐proteobacteria class; however, bacterial species diversity increases as Nasonia develop into pupae and adults. Finally, under identical environmental conditions, the relationships of the microbial communities reflect the phylogeny of the Nasonia host species at multiple developmental stages, which suggests that the structure of an animal's microbial community is closely allied with divergence of host genes. These findings highlight the importance of host evolutionary relationships on microbiota composition and have broad implications for future studies of microbial symbiosis and animal speciation.     

Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants

Microbial communities in plant roots provide critical links between above‐ and belowground processes in terrestrial ecosystems. Variation in root communities has been attributed to plant host effects and microbial host preferences, as well as to factors pertaining to soil conditions, microbial biogeography and the presence of viable microbial propagules. To address hypotheses regarding the influence of plant host and soil biogeography on root fungal and bacterial communities, we designed a trap‐plant bioassay experiment. Replicate Populus, Quercus and Pinus plants were grown in three soils originating from alternate field sites. Fungal and bacterial community profiles in the root of each replicate were assessed through multiplex 454 amplicon sequencing of four loci (i.e., 16S, SSU, ITS, LSU rDNA). Soil origin had a larger effect on fungal community composition than did host species, but the opposite was true for bacterial communities. Populus hosted the highest diversity of rhizospheric fungi and bacteria. Root communities on Quercus and Pinus were more similar to each other than to Populus. Overall, fungal root symbionts appear to be more constrained by dispersal and biogeography than by host availability.     

Temporal Dynamics of Bacterial and Fungal Communities in a Genetically Modified (GM) Rice Ecosystem

We assessed the temporal dynamics of bacterial and fungal communities in a soil ecosystem supporting genetically modified (GM) rice (Oryza sativa L., ABC-TPSP; fusion of trehalose-6-phosphate synthase and phosphatase). Using terminal restriction fragment length polymorphism analysis and real-time quantitative PCR, we compared bacterial and fungal communities in the soils underlying GM rice (ABC-TPSP), and its host cultivar (Nakdong) during growing seasons and non-growing seasons. Overall, the soils supporting GM and non-GM rice did not differ significantly in diversity indices, including ribotype numbers, for either bacteria or fungi. The diversity index (H) in both the bacterial and fungal communities was correlated with water content, dissolved organic carbon (DOC), and ammonium nitrogen, and the correlation was stronger in fungi than in bacteria. Multivariate analysis showed no differences in microbial community structures between the two crop genotypes, but such differences did appear in time, with significant changes observed after harvest. Gene copy number was estimated as 10⁸~10¹¹ and 10⁵~10⁷ per gram of soil for bacteria and fungi, respectively. As observed for community structure, the rice genotypes did not differ significantly in either bacterial- or fungal-specific gene copy numbers, although we observed a seasonal change in number. We summarize the results of this study as follows. (1) GM rice did not influence soil bacterial and fungal community structures as compared to non-GM rice in our system, (2) both bacterial and fungal communities changed with the growth stage of either rice genotype, (3) fungal communities were less variable than bacterial communities, and (4) although several environmental factors, including ammonium nitrogen and DOC correlated with shifts in microbial community structure, no single factor stood out.     

Sugar Beet-Associated Bacterial and Fungal Communities Show a High Indigenous Antagonistic Potential Against Plant Pathogens

The aim of this study was to analyze microbial communities in/on sugar beet with special focus on antagonists toward plant pathogens. For this purpose, the composition of microorganisms isolated from the rhizosphere, phyllosphere, endorhiza, and endosphere of field-grown sugar beet plants was analyzed by a multiphasic approach at three different plant development stages at six locations in Europe. The analysis of microbial communities by Single Strand Conformation Polymorphism (SSCP) of 16S/18S rRNA clearly revealed the existence of discrete microenvironment- and site-specific patterns. A total of 1952 bacterial and 1344 fungal isolates screened by dual testing for antagonism toward the pathogens Aphanomyces cochlioides, Phoma betae, Pythium ultimum, and Rhizoctonia solani resulted in 885 bacterial (=45%) and 437 fungal (=33%) antagonists. In general, the indigenous antagonistic potential was very high and influenced by (a) the location, (b) the plant developmental stage, and (3) the microenvironment. Furthermore, we showed for the first time that the antagonistic potential was highly specific for each target pathogen. The majority of antagonistic microorganisms suppressed only one pathogen (bacteria: 664 = 75%; fungi: 256 = 59%), whereas the minority showed a broad host range (bacteria: 4 = 0.5%; fungi: 7 = 1.6%). The bacterial communities harbored the highest antagonistic potential against P. ultimum, whereas the fungal communities contained more antagonists against A. cochlioides and R. solani. In contrast to their high proportion, only a low diversity of antagonists at genotypic and species level was found. Novel antagonistic species, e.g., Subtercola pratensis or Microbacterium testaceum were found in the internal part of the sugar beet body.     

Dynamics of bacterial and fungal communities on decaying salt marsh grass

Both bacteria and fungi play critical roles in decomposition processes in many natural environments, yet only rarely have they been studied as an integrated microbial community. Here we describe the bacterial and fungal assemblages associated with two decomposition stages of Spartina alterniflora detritus in a productive southeastern U.S. salt marsh. 16S rRNA genes and 18S-to-28S internal transcribed spacer (ITS) regions were used to target the bacterial and ascomycete fungal communities, respectively, based on DNA sequence analysis of isolates and environmental clones and by using community fingerprinting based on terminal restriction fragment length polymorphism (T-RFLP) analysis. Seven major bacterial taxa (six affiliated with the alpha-Proteobacteria and one with the Cytophagales) and four major fungal taxa were identified over five sample dates spanning 13 months. Fungal terminal restriction fragments (T-RFs) were informative at the species level; however, bacterial T-RFs frequently comprised a number of related genera. Amplicon abundances indicated that the salt marsh saprophyte communities have little-to-moderate variability spatially or with decomposition stage, but considerable variability temporally. However, the temporal variability could not be readily explained by either successional shifts or simple relationships with environmental factors. Significant correlations in abundance (both positive and negative) were found among dominant fungal and bacterial taxa that possibly indicate ecological interactions between decomposer organisms. Most associations involved one of four microbial taxa: two groups of bacteria affiliated with the alpha-Proteobacteria and two ascomycete fungi (Phaeosphaeria spartinicola and environmental isolate "4clt").     

Archaea and Fungi of the Human Gut Microbiome: Correlations with Diet and Bacterial Residents

Diet influences health as a source of nutrients and toxins, and by shaping the composition of resident microbial populations. Previous studies have begun to map out associations between diet and the bacteria and viruses of the human gut microbiome. Here we investigate associations of diet with fungal and archaeal populations, taking advantage of samples from 98 well-characterized individuals. Diet was quantified using inventories scoring both long-term and recent diet, and archaea and fungi were characterized by deep sequencing of marker genes in DNA purified from stool. For fungi, we found 66 genera, with generally mutually exclusive presence of either the phyla Ascomycota or Basiodiomycota. For archaea, Methanobrevibacter was the most prevalent genus, present in 30% of samples. Several other archaeal genera were detected in lower abundance and frequency. Myriad associations were detected for fungi and archaea with diet, with each other, and with bacterial lineages. Methanobrevibacter and Candida were positively associated with diets high in carbohydrates, but negatively with diets high in amino acids, protein, and fatty acids. A previous study emphasized that bacterial population structure was associated primarily with long-term diet, but high Candida abundance was most strongly associated with the recent consumption of carbohydrates. Methobrevibacter abundance was associated with both long term and recent consumption of carbohydrates. These results confirm earlier targeted studies and provide a host of new associations to consider in modeling the effects of diet on the gut microbiome and human health.