Comparison of fungal communities associated with spruce seedling roots and bryophyte carpets on logs in an old-growth subalpine coniferous forest in Japan

Fungal communities associated with plant tissues were compared between two bryophyte species dominating decaying logs (Scapania bolanderi and Pleurozium schreberi), and roots of spruce seedlings growing on the bryophytes and in the ground soil, to evaluate the contribution of fungal communities to seedling regeneration. Using high-throughput DNA sequencing, a total of 1233 fungal operational taxonomic units (OTUs) were detected. Saprotrophic Ascomycota were dominant in bryophytes, whereas ectomycorrhizal (ECM) Basidiomycota were dominant in spruce roots. Fungal communities were significantly different between the two bryophyte species. In addition, fungal communities of spruce seedlings were significantly affected by the substrates on which they were growing. Some ECM fungi were detected from both of the bryophytes and the spruce seedlings growing on them; however, the dominant OTU identities differed between the two bryophyte systems. The possible effects of functional differences between dominant fungal OTUs on spruce seedling regeneration are discussed.     

Communities of wood-inhabiting fungi in dead pine logs along a geographical gradient in Japan

Fungi are the main agents of coarse woody debris decomposition in forest ecosystems. We examined the associations of environmental variables with fungal community structures in dead pine logs at 12 geographically distant sites using amplicon pyrosequencing of fungal ITS rDNA. A total of 575 operational taxonomic units (OTUs) were identified based on clustering at 97% similarity. Among the known fungal ecological groups, saprotrophic fungi generally showed highest frequency of occurrence and were positively associated with mean annual temperature (MAT) and log diameter. Wood decay fungi with unknown decay type were positively associated with pine wilt disease and negatively associated with log diameter. Ordination analysis of the 42 most prevalent OTUs showed that MAT and annual precipitation significantly explained the observed fungal community structure. These results suggested that climate conditions and site history differentially effect structure fungal communities in pine logs among different ecological groups.     

Soil-wood interactions: Influence of decaying coniferous and broadleaf logs on composition of soil fungal communities

Wood-inhabiting fungi may affect soil fungal communities directly underneath decaying wood via their exploratory hyphae. In addition, differences in wood leachates between decaying tree species may influence soil fungal communities. We determined the composition of fungi in 4-yr old decaying logs of Larix kaempferi and Quercus rubra as well as in soil directly underneath and next to logs. Fungal community composition in soil covered by logs was different from that in wood and uncovered soil and was clearly influenced by the tree species. Soil fungal species richness under logs was lower than in uncovered soil but higher than in decaying wood. The amount of exploratory hyphae of log-inhabiting fungi was only high close to decaying logs. In conclusion, there is a small but significant effect of decaying coniferous and broadleaf logs on soil fungal communities directly underneath logs, likely affected by differences in wood chemistry and fungal preference between tree species.     

Fungi ahoy! Diversity on marine wooden substrata in the high North

Marine fungi are severely understudied in the polar regions. We used molecularly identified cultures to study fungi inhabiting 50 intertidal and sea-floor logs along the North Norwegian coast. The aim was to explore the taxonomic and ecological diversity and to examine factors shaping the marine wood-inhabiting fungal communities. The 577 pure cultures analyzed clustered into 147 operational taxonomic units (OTUs) based on 97 % ITS sequence similarity. Ascomycota dominated, but OTUs belonging to Basidiomycota, Mucoromycotina and Chytridiomycota were also isolated. Nine OTUs could not be assigned to any fungal phylum. Almost half of the OTUs were considered non-marine. The western and eastern part of the Norwegian Barents Sea coast hosted different communities. Geography, substratum and site level variables contributed to shaping these communities. We characterized a previously overlooked fungal community in a poorly studied area, discovered high diversity and report many taxa for the first time from the marine environment.     

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

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

Fungal palaeodiversity revealed using high‐throughput metabarcoding of ancient DNA from arctic permafrost

The taxonomic and ecological diversity of ancient fungal communities was assessed by combining next generation sequencing and metabarcoding of DNA preserved in permafrost. Twenty‐six sediment samples dated 16 000–32 000 radiocarbon years old from two localities in Siberia were analysed for fungal ITS. We detected 75 fungal OTUs from 21 orders representing three phyla, although rarefaction analyses suggested that the full diversity was not recovered despite generating an average of 6677 ± 3811 (mean ± SD) sequences per sample and that preservation bias likely has considerable effect on the recovered DNA. Most OTUs (75.4%) represented ascomycetes. Due to insufficient sequencing depth, DNA degradation and putative preservation biases in our samples, the recovered taxa probably do not represent the complete historic fungal community, and it is difficult to determine whether the fungal communities varied geographically or experienced a composition shift within the period of 16 000–32 000 bp . However, annotation of OTUs to functional ecological groups provided a wealth of information on the historic communities. About one‐third of the OTUs are presumed plant‐associates (pathogens, saprotrophs and endophytes) typical of graminoid‐ and forb‐rich habitats. We also detected putative insect pathogens, coprophiles and keratinophiles likely associated with ancient insect and herbivore faunas. The detection of putative insect pathogens, mycoparasites, aquatic fungi and endophytes broadens our previous knowledge of the diversity of fungi present in Beringian palaeoecosystems. A large group of putatively psychrophilic/psychrotolerant fungi was also detected, most likely representing a modern, metabolically active fungal community.     

Soil fungal communities in a Castanea sativa (chestnut) forest producing large quantities of Boletus edulis sensu lato (porcini): where is the mycelium of porcini?

A study was conducted in a Castanea sativa forest that produces large quantities of the edible mushroom porcini (Boletus edulis sensu lato). The primary aim was to study porcini mycelia in the soil, and to determine if there were any possible ecological and functional interactions with other dominant soil fungi. Three different approaches were used: collection and morphological identification of fruiting bodies, morphological and molecular identification of ectomycorrhizae by rDNA-ITS sequence analyses and molecular identification of the soil mycelia by ITS clone libraries. Soil samples were taken directly under basidiomes of Boletus edulis, Boletus aestivalis, Boletus aereus and Boletus pinophilus. Thirty-nine ectomycorrhizal fungi were identified on root tips whereas 40 fungal species were found in the soil using the cloning technique. The overlap between above- and below-ground fungal communities was very low. Boletus mycelia, compared with other soil fungi, were rare and with scattered distribution, whereas their fruiting bodies dominated the above-ground fungal community. Only B. aestivalis ectomycorrhizae were relatively abundant and detected as mycelia in the soil. No specific fungus-fungus association was found. Factors triggering formation of mycorrhizae and fructification of porcini appear to be too complex to be simply explained on the basis of the amount of fungal mycelia in the soil.     

Characterization of fungal communities associated with the bark beetle Ips typographus varies depending on detection method, location, and beetle population levels

The Eurasian spruce bark beetle Ips typographus and their fungal associates can cause severe damage to Norway spruce forests. In this paper, by using both molecular and cultural methods, we compared fungal assemblages on bark beetles from different locations, characterized by different beetle population levels. Ips typographus was trapped in the western Alps in two outbreak and in two control areas. Sequencing of clone libraries of Internal Transcribed Spacer (ITS) identified 31 fungal Operational Taxonomic Units (OTUs), while fungal isolations yielded 55 OTUs. Only three OTUs were detected by both molecular and cultural methods indicating that both methods are necessary to adequately describe fungal richness. Fungal assemblages on insects from these four and from an additional 12 study sites differed among stands in response to varying ecological conditions and to the limited spreading ability of I. typographus. Ophiostomatoid fungi showed higher diversity in outbreak areas; the pathogenic Ophiostoma polonicum was relatively uncommon, while O. bicolor was the most abundant species. This result was not unexpected, as insects were trapped not at the peak but at the end of the outbreaks and supports the hypothesis of a temporal succession among Ophiostoma species. Ubiquitous endophytes of trees or common airborne fungi were present both in outbreak and in control areas. Wood decaying basidiomycetes were almost never detected on beetles. Yeasts were detected only by molecular analysis, and the OTUs detected matched those reported elsewhere in Europe and in the world, suggesting a very long association between some yeasts and bark beetles.     

Fungal diversity within the phyllosphere of Pinus massoniana and the possible involvement of phyllospheric fungi in litter decomposition

Fungi play key roles in forest ecosystems and help to shape the forest’s diverse functions. However, little is known about the diversity of phyllospheric fungi or their possible relationships with fungal communities residing in different micro-environments of Pinus massoniana forests. We investigated seven different sample types: mature needles (NM), dead needles (ND), needles falling as litter (L), fermenting needles (F), humus (H), top soil (0–20 cm) (TS), and secondary soil (20–40 cm) (SS). These seven fungal communities were examined and compared with ITS amplicons using a high-throughput sequencing technique. A total of 1213 fungal operational taxonomic units (OTUs) were obtained at a 97% sequence similarity level. Distinct fungal communities were associated with different sample types. A greater number of OTUs were present in both NM and F samples than those shared by both NM and TS samples, indicating that phyllospheric fungi may play crucial roles in litter decomposition. Sixty OTUs (the core microbiome) were found in all sample types, and they may probably play different ecological roles in different sample types. These findings extend our knowledge of the fungal diversity of the phyllosphere and its possible interactions with fungal communities found in distinct forest micro-habitats.     

High consistency between replicate 454 pyrosequencing analyses of ectomycorrhizal plant root samples

In this methodological study, we compare 454 sequencing and a conventional cloning and Sanger sequencing approach in their ability to characterize fungal communities PCR amplified from four root systems of the ectomycorrhizal plant Bistorta vivipara. To examine variation introduced by stochastic processes during the laboratory work, we replicated all analyses using two independently obtained DNA extractions from the same root systems. The ITS1 region was used as DNA barcode and the sequences were clustered into OTUs as proxies for species using single linkage clustering (BLASTClust) and 97% sequence similarity cut-off. A relatively low overlap in fungal OTUs was observed between the 454 and the clone library datasets — even among the most abundant OTUs. In a non-metric multidimensional scaling analysis, the samples grouped more according to methodology compared to plant. Some OTUs frequently detected by 454, most notably those OTUs with taxonomic affinity to Glomales, were not detected in the Sanger dataset. Likewise, a few OTUs, including Cenococcum sp., only appeared in the clone libraries. Surprisingly, we observed a significant relationship between GC/AT content of the OTUs and their proportional abundances in the 454 versus the clone library datasets. Reassuringly, a very good consistency in OTU recovery was observed between replicate runs of both sequencing methods. This indicates that stochastic processes had little impact when applying the same sequencing technique on replicate samples.     

Molecular profiling of rhizosphere microbial communities associated with healthy and diseased black spruce (Picea mariana) seedlings grown in a nursery

Bacterial and fungal populations associated with the rhizosphere of healthy black spruce (Picea mariana) seedlings and seedlings with symptoms of root rot were characterized by cloned rRNA gene sequence analysis. Triplicate bacterial and fungal rRNA gene libraries were constructed, and 600 clones were analyzed by amplified ribosomal DNA restriction analysis and grouped into operational taxonomical units (OTUs). A total of 84 different bacterial and 31 different fungal OTUs were obtained and sequenced. Phylogenetic analyses indicated that the different OTUs belonged to a wide range of bacterial and fungal taxa. For both groups, pairwise comparisons revealed that there was greater similarity between replicate libraries from each treatment than between libraries from different treatments. Significant differences between pooled triplicate samples from libraries of genes from healthy seedlings and pooled triplicate samples from libraries of genes from diseased seedlings were also obtained for both bacteria and fungi, clearly indicating that the rhizosphere-associated bacterial and fungal communities of healthy and diseased P. mariana seedlings were different. The communities associated with healthy and diseased seedlings also showed distinct ecological parameters as indicated by the calculated diversity, dominance, and evenness indices. Among the main differences observed at the community level, there was a higher proportion of Acidobacteria, Gammaproteobacteria, and Homobasidiomycetes clones associated with healthy seedlings, while the diseased-seedling rhizosphere harbored a higher proportion of Actinobacteria, Sordariomycetes, and environmental clones. The methodological approach described in this study appears promising for targeting potential rhizosphere-competent biological control agents against root rot diseases occurring in conifer nurseries.     

Bacterial diversity and community composition from seasurface to subseafloor

We investigated compositional relationships between bacterial communities in the water column and those in deep-sea sediment at three environmentally distinct Pacific sites (two in the Equatorial Pacific and one in the North Pacific Gyre). Through pyrosequencing of the v4–v6 hypervariable regions of the 16S ribosomal RNA gene, we characterized 450 104 pyrotags representing 29 814 operational taxonomic units (OTUs, 97% similarity). Hierarchical clustering and non-metric multidimensional scaling partition the samples into four broad groups, regardless of geographic location: a photic-zone community, a subphotic community, a shallow sedimentary community and a subseafloor sedimentary community (⩾1.5 meters below seafloor). Abundance-weighted community compositions of water-column samples exhibit a similar trend with depth at all sites, with successive epipelagic, mesopelagic, bathypelagic and abyssopelagic communities. Taxonomic richness is generally highest in the water-column O₂ minimum zone and lowest in the subseafloor sediment. OTUs represented by abundant tags in the subseafloor sediment are often present but represented by few tags in the water column, and represented by moderately abundant tags in the shallow sediment. In contrast, OTUs represented by abundant tags in the water are generally absent from the subseafloor sediment. These results are consistent with (i) dispersal of marine sedimentary bacteria via the ocean, and (ii) selection of the subseafloor sedimentary community from within the community present in shallow sediment.     

不同扩增引物对高通量测序分析盐角草内生真菌多样性的影响

【背景】高通量测序分析作为深入了解环境微生物群落组成的重要方法,已成为植物内生真菌多样性研究的有效手段,然而由于引物的扩增差异,采用不同引物可对实验结果分析造成影响。同时,盐角草作为世界上最耐盐的植物之一,存在着多种功能性的内生真菌,而较为全面介绍其内生真菌组成和多样性的报道鲜见。【目的】为了揭示盐角草内生真菌的多样性,解析不同扩增引物对内生菌多样性分析的影响。【方法】分别采用真菌高通量测序常用引物对ITS1-5F、ITS1-1F、ITS2对采自乌鲁木齐达坂城盐湖的盐角草内生真菌进行扩增,开展其内生真菌OTU的分析。【结果】通过不同引物对扩增并测序共获得102个盐角草内生真菌OTU,涉及真菌界8个门和未分类菌群,其中子囊菌门(Ascomycota)占绝对优势,其次为担子菌门(Basidiomycota);在属层次上,盐角草内生真菌共涉及64个属及20个未分类属,其中Alternaria、Cladosporium、Podospora等3个属为盐角草内生真菌优势菌群。对不同引物对扩增测序结果分析表明,不同引物对扩增对分析内生真菌OTU数量和种类具有明显的影响,在全部所得的102个OTU中,ITS1-5F引物对获得44个OTU、ITS1-1F引物对获得55个OTU、ITS2引物对获得25个OTU,但以上3对引物扩增均检测到的OTU数仅为5个。物种组成和多样性分析表明,内生真菌多样性分析中采用以ITS1-1F为主,ITS1-5F为辅的分析策略,可较为全面地展现内生真菌的多样性。【结论】盐角草存在较为丰富的内生真菌资源,不同扩增引物对高通量分析盐角草内生真菌组成和分布具有明显的影响。     

Cellulose utilization in forest litter and soil: identification of bacterial and fungal decomposers

Organic matter decomposition in the globally widespread coniferous forests has an important role in the carbon cycle, and cellulose decomposition is especially important in this respect because cellulose is the most abundant polysaccharide in plant litter. Cellulose decomposition was 10 times faster in the fungi-dominated litter of Picea abies forest than in the bacteria-dominated soil. In the soil, the added (13)C-labelled cellulose was the main source of microbial respiration and was preferentially accumulated in the fungal biomass and cellulose induced fungal proliferation. In contrast, in the litter, bacterial biomass showed higher labelling after (13)C-cellulose addition and bacterial biomass increased. While 80% of the total community was represented by 104-106 bacterial and 33-59 fungal operational taxonomic units (OTUs), 80% of the cellulolytic communities of bacteria and fungi were only composed of 8-18 highly abundant OTUs. Both the total and (13)C-labelled communities differed substantially between the litter and soil. Cellulolytic bacteria in the acidic topsoil included Betaproteobacteria, Bacteroidetes and Acidobacteria, whereas these typically found in neutral soils were absent. Most fungal cellulose decomposers belonged to Ascomycota; cellulolytic Basidiomycota were mainly represented by the yeasts Trichosporon and Cryptococcus. Several bacteria and fungi demonstrated here to derive their carbon from cellulose were previously not recognized as cellulolytic.     

Molecular Profiling of Rhizosphere Microbial Communities Associated with Healthy and Diseased Black Spruce (Picea mariana) Seedlings Grown in a Nursery

Bacterial and fungal populations associated with the rhizosphere of healthy black spruce (Picea mariana) seedlings and seedlings with symptoms of root rot were characterized by cloned rRNA gene sequence analysis. Triplicate bacterial and fungal rRNA gene libraries were constructed, and 600 clones were analyzed by amplified ribosomal DNA restriction analysis and grouped into operational taxonomical units (OTUs). A total of 84 different bacterial and 31 different fungal OTUs were obtained and sequenced. Phylogenetic analyses indicated that the different OTUs belonged to a wide range of bacterial and fungal taxa. For both groups, pairwise comparisons revealed that there was greater similarity between replicate libraries from each treatment than between libraries from different treatments. Significant differences between pooled triplicate samples from libraries of genes from healthy seedlings and pooled triplicate samples from libraries of genes from diseased seedlings were also obtained for both bacteria and fungi, clearly indicating that the rhizosphere-associated bacterial and fungal communities of healthy and diseased P. mariana seedlings were different. The communities associated with healthy and diseased seedlings also showed distinct ecological parameters as indicated by the calculated diversity, dominance, and evenness indices. Among the main differences observed at the community level, there was a higher proportion of Acidobacteria, Gammaproteobacteria, and Homobasidiomycetes clones associated with healthy seedlings, while the diseased-seedling rhizosphere harbored a higher proportion of Actinobacteria, Sordariomycetes, and environmental clones. The methodological approach described in this study appears promising for targeting potential rhizosphere-competent biological control agents against root rot diseases occurring in conifer nurseries.     

Water mass-specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing

Bacterial assemblages from subsurface (100 m depth), meso- (200-1000 m depth) and bathy-pelagic (below 1000 m depth) zones at 10 stations along a North Atlantic Ocean transect from 60°N to 5°S were characterized using massively parallel pyrotag sequencing of the V6 region of the 16S rRNA gene (V6 pyrotags). In a dataset of more than 830,000 pyrotags, we identified 10,780 OTUs of which 52% were singletons. The singletons accounted for less than 2% of the OTU abundance, whereas the 100 and 1000 most abundant OTUs represented 80% and 96% respectively of all recovered OTUs. Non-metric Multi-Dimensional Scaling and Canonical Correspondence Analysis of all the OTUs excluding the singletons revealed a clear clustering of the bacterial communities according to the water masses. More than 80% of the 1000 most abundant OTUs corresponded to Proteobacteria of which 55% were Alphaproteobacteria, mostly composed of the SAR11 cluster. Gammaproteobacteria increased with depth and included a relatively large number of OTUs belonging to Alteromonadales and Oceanospirillales. The bathypelagic zone showed higher taxonomic evenness than the overlying waters, albeit bacterial diversity was remarkably variable. Both abundant and low-abundance OTUs were responsible for the distinct bacterial communities characterizing the major deep-water masses. Taken together, our results reveal that deep-water masses act as bio-oceanographic islands for bacterioplankton leading to water mass-specific bacterial communities in the deep waters of the Atlantic.     

蝉棒束孢内菌核、菌膜及其生境土壤真菌群落结构及生态功能分析

通过分析蝉棒束孢Isaria cicadae内菌核、菌膜及其生境土壤的真菌群落结构与核心真菌组的生态功能,初步探索蝉棒束孢自然生长过程中内环境真菌与其周围环境中真菌的关系。本研究利用高通量测序技术检测6株采自贵阳大将山和贵阳森林公园的蝉棒束孢及土壤样本,结果表明,蝉棒束孢内菌核共检测到43个真菌属,菌膜检测到58个真菌属,菌际土检测到260个真菌属,且内菌核和菌膜真菌群落结构相似。而两地生境土的真菌群落结构有差异,大将山以棒束孢属Isaria、被孢霉属Mortierella和一分类地位未知属占优势,而贵阳森林公园以被孢霉属、隐球酵母属Cryptococcus、红菇属Russula、棒束孢属占优势,且两地菌际土中棒束孢属的丰度均显著高于其他土样。核心真菌组检测分析显示,内菌核的核心真菌组有10个OTUs,菌膜的核心真菌组有5个OTUs,菌际土的核心真菌组有20个OTUs,3种样本的核心真菌组的生态功能群均检测到有与植物相关的功能群,内菌核中检测到外生菌根真菌群,菌膜中检测到植物病原真菌群,菌际土中检测到丛枝菌根真菌群和植物病原菌群。     

Is fungal species richness and composition related to the occurrence of the old‐growth associated wood‐decaying Amylocystis lapponica?

Amylocystis lapponica (Romell) Singer is a widely distributed wood‐decaying polypore fungus found throughout the Northern Hemisphere. Despite its huge distribution range it occurs rather patchily and seems narrowly associated with old‐growth forest stands. Notably, it has been used as an ‘indicator species’, believed to reflect the long‐term presence of dead wood, naturalness of forest stands, and indirectly, species richness and possibly composition. In this study we focused on the last issue – whether or not there is a link between the occurrence of A. lapponica and the species richness and composition of other wood‐decaying fungi. Selecting log characteristics and microclimate as similar as possible, we compared 12 logs with and 12 logs without visible fruit bodies of A. lapponica to examine: 1) if visible fruit bodies corresponded with molecular identification of the mycelia, 2) if fungal species richness and composition of the substrate were related to A. lapponica occurrence, and 3) if A. lapponica was restricted to certain parts of the log. Fungal species were recorded by inspecting visible fruit bodies and by culture isolation and ITS sequencing from wood disc samples. Laboratory and field identification of A. lapponica had 71% correspondence, and mycelia were identified in two logs without visible fruit bodies. Twice as many fungal species were detected using ITS sequencing compared to fruit body identification. Total species richness was similar between the two log categories, but number of species per log was slightly higher in A. lapponica logs. Antrodia serialis (Fr.) Donk, and possibly also Fomitopsis pinicola (Sw.:Fr.) P. Karst. and Phellinus nigrolimitatus (Romell) Bourdot & Galzin, occurred more frequently in A. lapponica logs. Mycelia of A. lapponica were restricted to less decayed parts of the wood in the centre of the middle part of the logs.     

Massive parallel 16S rRNA gene pyrosequencing reveals highly diverse fecal bacterial and fungal communities in healthy dogs and cats

This study evaluated the fecal microbiota of 12 healthy pet dogs and 12 pet cats using bacterial and fungal tag-encoded FLX-Titanium amplicon pyrosequencing. A total of 120,406 pyrosequencing reads for bacteria (mean 5017) and 5359 sequences (one pool each for dogs and cats) for fungi were analyzed. Additionally, group-specific 16S rRNA gene clone libraries for Bifidobacterium spp. and lactic acid-producing bacteria (LAB) were constructed. The most abundant bacterial phylum was Firmicutes, followed by Bacteroidetes in dogs and Actinobacteria in cats. The most prevalent bacterial class in dogs and cats was Clostridia, dominated by the genera Clostridium (clusters XIVa and XI) and Ruminococcus. At the genus level, 85 operational taxonomic units (OTUs) were identified in dogs and 113 OTUs in cats. Seventeen LAB and eight Bifidobacterium spp. were detected in canine feces. Ascomycota was the only fungal phylum detected in cats, while Ascomycota, Basidiomycota, Glomeromycota, and Zygomycota were identified in dogs. Nacaseomyces was the most abundant fungal genus in dogs; Saccharomyces and Aspergillus were predominant in cats. At the genus level, 33 different fungal OTUs were observed in dogs and 17 OTUs in cats. In conclusion, this study revealed a highly diverse bacterial and fungal microbiota in canine and feline feces.     

Global patterns of diversity and community structure in marine bacterioplankton

Because of their small size, great abundance and easy dispersal, it is often assumed that marine planktonic microorganisms have a ubiquitous distribution that prevents any structured assembly into local communities. To challenge this view, marine bacterioplankton communities from coastal waters at nine locations distributed world-wide were examined through the use of comprehensive clone libraries of 16S ribosomal RNA genes, used as operational taxonomic units (OTU). Our survey and analyses show that there were marked differences in the composition and richness of OTUs between locations. Remarkably, the global marine bacterioplankton community showed a high degree of endemism, and conversely included few cosmopolitan OTUs. Our data were consistent with a latitudinal gradient of OTU richness. We observed a positive relationship between the relative OTU abundances and their range of occupation, i.e. cosmopolitans had the largest population sizes. Although OTU richness differed among locations, the distributions of the major taxonomic groups represented in the communities were analogous, and all local communities were similarly structured and dominated by a few OTUs showing variable taxonomic affiliations. The observed patterns of OTU richness indicate that similar evolutionary and ecological processes structured the communities. We conclude that marine bacterioplankton share many of the biogeographical and macroecological features of macroscopic organisms. The general processes behind those patterns are likely to be comparable across taxa and major global biomes.