Metal-Tolerant Fungal Communities Are Delineated by High Zinc, Lead, and Copper Concentrations in Metalliferous Gobi Desert Soils.

The soil fungal ecology of the southern Gobi region of Mongolia has been little studied. We utilized the ITS1 region from soil DNA to study possible influences soil metal concentrations on soil fungal community variation. In the sample network, a distinctive fungal community was closely associated with high zinc (Zn), lead (Pb), and copper (Cu) concentrations. The pattern of occurrence suggests that high metal concentrations are natural and not a product of mining activities. The metal-associated fungal community differs little from the "normal" community in its major OTUs, and in terms of major fungal guilds and taxa, and its distinctiveness depends on a combination of many less common OTUs. The fungal community in the sites with high metal concentrations is no less diverse than that in areas with normal background levels. Overall, these findings raise interesting questions of the evolutionary origin and functional characteristics of this apparently "metal-tolerant" community, and of the associated soil biota in general. It is possible that rehabilitation of metal-contaminated mined soils from spoil heaps could benefit from the incorporation of fungi derived from these areas.

Morphological characterization and first molecular identification of the eleven Eimeria species that infect sheep from Mexico.

Within livestock production, enteric diseases play an important role, since they cause severe economic losses due to mortality, growth depression, and reduction in the conversion rate. Coccidiosis caused by Eimeria spp. is a parasitic disease of high morbidity that affects various animal species, including sheep. In sheep, eleven species of Eimeria have been identified mainly through microscopical identification of the oocysts; however, this technique has certain limitations that make it difficult to identify the different Eimeria species. The objective of the present study was to morphologically identify the eleven species of Eimeria that infect sheep in the southeastern region of the State of Mexico, as well as obtain the partial sequence of the ITS-1 rRNA region of each species and analyze it phylogenetically. A total of 412 samples were collected from the 13 municipalities that comprise the region I of the State of Mexico, out of which, 40 had approximately 80% of a single Eimeria species. Among these, the eleven Eimeria species reported in sheep were identified. The phylogenetic analysis showed that the species reported in this study are associated with those reported in rabbits, bovines, and birds. It is suggested that the phylogenetic division of sheep in two clades may be associated with the presence or absence of the residual body. It is proposed that the present methodology can be used effectively for diagnosis and to obtain information about the epidemiology of ovine coccidial infection. The results obtained in this study constitute the first report of the ITS-1 region of the eleven Eimeria species that infect sheep worldwide.

Characterization of fungal microbial diversity in Tibetan sheep, Tibetan gazelle and Tibetan antelope in the Qiangtang region of Tibet.

Due to the high crude fiber content, straw of various crops is difficult to become a high quality forage resource. The degradation of cellulose in nature mainly depends on the cellulase secreted by microbes, which degrade cellulose into small molecular substances through chemical action, and the microbes that secrete cellulase mainly include some bacteria, fungi and actinomycetes, etc. The large and diverse microbial population contained in the mammalian gastrointestinal tract plays an important role in nutrient digestion. At present, many cellulose-degrading strains have been screened and obtained from animal digestive system and feces, such as Bacillus subtilis from the feces of Panda, Bacillus amyloliquefaciens from the cecum of goose. In this study, the fungal diversity was analysed in the fresh faeces of Tibetan sheep, Tibetan gazelle and Tibetan antelope in Qiangtang, Tibet. Results showed that the structure and species of gut fungi are different in three animals, which may be related to the different physiological functions among different animals, e.g., Tibetan antelope and Tibetan gazelle have stronger tolerance to rough feeding than Tibetan sheep. This study will lay a foundation for cellulose-degrading fungal development and provides technical support for improving rough feeding tolerance of Tibetan sheep.

Morphological description and molecular characterisation of Dactylogyrus matlopong sp. n. (Monogenea: Dactylogyridae) from the South African endemic Labeobarbus aeneus (Cyprinidae: Torinae).

Dactylogyrus Diesing, 1850 is the most species-rich genus in Platyhelminthes, with over 900 documented species, that are mostly strictly specific to freshwater cyprinoids. The morphological Dactylogyrus groups afrobarbae-type, carpathicus-type, pseudoanchoratus-type, and varicorhini-type are known to occur in Africa. This study describes a new species of Dactylogyrus of the varicorhini-type from the gills of the endemic smallmouth yellowfish Labeobarbus aeneus (Burchell) from the Vaal River, Free State Province, South Africa. Dactylogyrus matlopong sp. n. is unique among its varicorhini-type congeners mainly by the accessory piece of the male copulatory complex that presents a hook-shaped subunit with defined round base not reaching the male copulatory organ, combined with the presence of a conspicuous medial projection on the anterior margin of the ventral bar. Sequences of the partial 28S and 18S rRNA genes, together with entire ITS1 region, were generated for the first time for a species of Dactylogyrus from South Africa. Concatenated phylogenetic analyses of selected Dactylogyrus spp. showed that these parasites group according to their morphological types.

Disentangling the structure and function of mycoplankton communities in the context of marine environmental heterogeneity.

Mycoplankton are a diverse and ubiquitous component of marine environments with a suggested role in ocean biogeochemical cycling. Thus far, the patterns of their abundance, structure, and function against spatial environmental heterogeneity remains poorly understood. Based on in silico and experimental evaluation of multiple markers, we adopted the ITS1 region to determine the composition, guilds, and metabolic potential of mycoplankton communities in contrasting marine environments. The trophic status of estuarine (SB1 and SB2) and coastal (DB1 and DB2) sites, but not oceanic (OS) site, was the major factor that determined their abundances. While ascomycetous fungi dominated the estuarine and coastal sites, basidiomycetous fungi were found to dominate the oceanic site. The zoosporic fungi were relatively more abundant in SB1 and DB2 sites compared to the other sites. The relative abundances of the core fungi, namely Cystobasidium, Phlebia, Rhodotorula, Trichoderma, Alternaria, Penicillium, Malassezia, and Aspergillus varied widely across the sites. Additionally, several fungal genera unique to each site were also identified. DB2 site exhibited the lowest fungal richness while the OS site the highest. Conversely, the diversity and evenness were the lowest for the OS site but highest for the SB1 site. Temperature, pH, and chlorophyll-a were strongly associated with spatial diversity patterns. Of the 11 assigned guilds, some guilds particularly were not detected, including plant pathogen-wood saprotroph in DB2, the endophyte-plant pathogen in OS, the animal pathogen in SB1, and fungal parasite in DB1 and SB2. Within core functions-metabolism of amino acids, carbohydrates and energy, fatty acids and lipids, nitrogen, sulfur, and other compounds-several pathways showed spatial variations. Overall, this study not just broadens the taxonomic and metabolic repertoire of marine mycoplankton but also provides the first evidence of how these are shaped by site-scale environmental heterogeneity.

Inferences in microbial structural signatures of acne microbiome and mycobiome.

Acne vulgaris, commonly known as acne, is the most common skin disorder and a multifactorial disease of the sebaceous gland. Although the pathophysiology of acne is still unclear, bacterial and fungal factors are known to be involved in. This study aimed to investigate whether the microbiomes and mycobiomes of acne patients are distinct from those of healthy subjects and to identify the structural signatures of microbiomes related to acne vulgaris. A total of 33 Korean female subjects were recruited (Acne group, n = 17; Healthy group, n = 16), and microbiome samples were collected swabbing the forehead and right cheek. To characterize the fungal and bacterial communities, 16S rRNA V4-V5 and ITS1 region, respectively, were sequenced and analysed using Qiime2. There were no significant differences in alpha and beta diversities of microbiomes between the Acne and Healthy groups. In comparison with the ratio of Cutibacterium to Staphylococcus, the acne patients had higher abundance of Staphylococcus compared to Cutibacterium than the healthy individuals. In network analysis with the dominant microorganism amplicon sequence variants (ASV) (Cutibacterium, Staphylococcus, Malassezia globosa, and Malassezia restricta) Cutibacterium acnes was identified to have hostile interactions with Staphylococcus and Malassezia globosa. Accordingly, this results suggest an insight into the differences in the skin microbiome and mycobiome between acne patients and healthy controls and provide possible microorganism candidates that modulate the microbiomes associated to acne vulgaris.

Assessing the relationship between the rumen microbiota and feed efficiency in Nellore steers.

BACKGROUND: Ruminants rely upon a complex community of microbes in their rumen to convert host-indigestible feed into nutrients. However, little is known about the association between the rumen microbiota and feed efficiency traits in Nellore (Bos indicus) cattle, a breed of major economic importance to the global beef market. Here, we compare the composition of the bacterial, archaeal and fungal communities in the rumen of Nellore steers with high and low feed efficiency (FE) phenotypes, as measured by residual feed intake (RFI). RESULTS: The Firmicutes to Bacteroidetes ratio was significantly higher (P < 0.05) in positive-RFI steers (p-RFI, low feed efficiency) than in negative-RFI (n-RFI, high feed efficiency) steers. The differences in bacterial composition from steers with high and low FE were mainly associated with members of the families Lachnospiraceae, Ruminococcaceae and Christensenellaceae, as well as the genus Prevotella. Archaeal community richness was lower (P < 0.05) in p-RFI than in n-RFI steers and the genus Methanobrevibacter was either increased or exclusive of p-RFI steers. The fungal genus Buwchfawromyces was more abundant in the rumen solid fraction of n-RFI steers (P < 0.05) and a highly abundant OTU belonging to the genus Piromyces was also increased in the rumen microbiota of high-efficiency steers. However, analysis of rumen fermentation variables and functional predictions indicated similar metabolic outputs for the microbiota of distinct FE groups. CONCLUSIONS: Our results demonstrate that differences in the ruminal microbiota of high and low FE Nellore steers comprise specific taxa from the bacterial, archaeal and fungal communities. Biomarker OTUs belonging to the genus Piromyces were identified in animals showing high feed efficiency, whereas among archaea, Methanobrevibacter was associated with steers classified as p-RFI. The identification of specific RFI-associated microorganisms in Nellore steers could guide further studies targeting the isolation and functional characterization of rumen microbes potentially important for the energy-harvesting efficiency of ruminants.

Interaction Between Conservation Tillage and Nitrogen Fertilization Shapes Prokaryotic and Fungal Diversity at Different Soil Depths: Evidence From a 23-Year Field Experiment in the Mediterranean Area.

Soil biodiversity accomplishes key roles in agro-ecosystem services consisting in preserving and enhancing soil fertility and nutrient cycling, crop productivity and environmental protection. Thus, the improvement of knowledge on the effect of conservation practices, related to tillage and N fertilization, on soil microbial communities is critical to better understand the role and function of microorganisms in regulating agro-ecosystems. In the Mediterranean area, vulnerable to climate change and suffering for management-induced losses of soil fertility, the impact of conservation practices on soil microbial communities is of special interest for building mitigation and adaptation strategies to climate change. A long-term experiment, originally designed to investigate the effect of tillage and N fertilization on crop yield and soil organic carbon, was utilized to understand the effect of these management practices on soil prokaryotic and fungal community diversity. The majority of prokaryotic and fungal taxa were common to all treatments at both soil depths, whereas few bacterial taxa (Cloacimonates, Spirochaetia and Berkelbacteria) and a larger number of fungal taxa (i.e., Coniphoraceae, Debaryomycetaceae, Geastraceae, Cordicypitaceae and Steccherinaceae) were unique to specific management practices. Soil prokaryotic and fungal structure was heavily influenced by the interaction of tillage and N fertilization: the prokaryotic community structure of the fertilized conventional tillage system was remarkably different respect to the unfertilized conservation and conventional systems in the surface layer. In addition, the effect of N fertilization in shaping the fungal community structure of the surface layer was higher under conservation tillage systems than under conventional tillage systems. Soil microbial community was shaped by soil depth irrespective of the effect of plowing and N addition. Finally, chemical and enzymatic parameters of soil and crop yields were significantly related to fungal community structure along the soil profile. The findings of this study gave new insights on the identification of management practices supporting and suppressing beneficial and detrimental taxa, respectively. This highlights the importance of managing soil microbial diversity through agro-ecological intensified systems in the Mediterranean area.

Effects of Hardwood Biochar on Methane Production, Fermentation Characteristics, and the Rumen Microbiota Using Rumen Simulation.

Biochar is a novel carbonized feed additive sourced from pyrolyzed biomass. This compound is known to adsorb gasses and carbon, participate in biological redox reactions and provide habitat biofilms for desirable microbiota proliferation. Therefore, biochar holds potential to modify rumen fermentation characteristics and reduce enteric CH4 emissions. The objective of this study was to investigate the effect of hardwood biochar supplementation on fermentation parameters, methane (CH4) production and the ruminal archaeal, bacterial, and fungal microbiota using the in vitro RUSITEC (rumen simulation technique) system. Treatments consisted of a control diet (oaten pasture: maize silage: concentrate, 35:35:30 w/w) and hardwood biochar included at 400 or 800 mg per day (3.6 and 7.2% of substrate DM, respectively), over a 15-day period. Biochar supplementation had no effect (P ≥ 0.37) on pH, effluent (mL/d), total gas (mL/d), dry matter (DM) digestibility or CH4 production (mg/d). The addition of 800 mg biochar per day had the tendency (P = 0.10) to lower the % of CH4 released in fermentation compared to 400 mg/d biochar treatment. However, no effect (P ≥ 0.44) was seen on total VFA, acetate, propionate, butyric, branched-chain VFA, valerate and caproate production and the ratio of acetate to propionate. No effect (P > 0.05) was observed on bacterial, archaeal or fungal community structure. However, biochar supplementation at 800 mg/d decreased the abundance of one Methanomethylophilaceae OTU (19.8-fold, P = 0.046) and one Lactobacillus spp. OTU (31.7-fold, P < 0.01), in comparison to control treatments. Two fungal OTUs classified as Vishniacozyma victoriae (5.4 × 107 increase) and Sporobolomyces ruberrimus (5.4 × 107-fold increase) were more abundant in the 800 mg/d biochar samples. In conclusion, hardwood biochar had no effects on ruminal fermentation characteristics and may potentially lower the concentration of enteric CH4 when included at higher dosages by manipulating ruminal microbiota abundances.

Diversity of Fungal Communities in Heshang Cave of Central China Revealed by Mycobiome-Sequencing.

Deciphering of the mycobiome in pristine karst caves has been impeded by constraints of remote locations, inaccessibility to specimens and technical limitations, which greatly restricted in-depth understanding of mycobiomes in subterranean ecosystem. Here, mycobiomes of Heshang Cave in south-western karst region of China were investigated by Illumina HiSeq sequencing of fungal rRNA-ITS1 gene across different habitats. In total 793,502 ITS1 reads and 2,179 OTUs from 778 Mb reads after stringent quality control (Q30) and 453 genera, 72 orders and 19 classes within 6 phyla were detected. Ascomycota (42% OTUs) dominated across the five habitats. Shannon-Wiener index varied from 1.25 to 7.62 and community richness was highest in drip waters, followed by weathered rocks, bat guanos, sediments, and air samples. Mycobiomes displayed specificity to five habitats and more distinct OTUs were found in weathered rocks (12%) and drip waters (9%). In contrast, only 6.60% core OTUs were shared by five habitats. Notably, weathered rocks possessed more indicator groups and were revealed for the first time to be dominated by Sordariomycetes (43%). The community richness of air mycobiomes increased from cave entrance to the innermost part and dominated by the indicator groups of Penicillium mallochii (>30%) and P. herquei (>9%). Our work represents the largest attempt to date to a systematical investigation of oligotrophic solution-cave-associated mycobiomes in China. Our discovery of high diversity of mycobiomes in Heshang Cave also suggests that eukaryotic microorganisms may play a crucial role in subsurface environments.

Molecular investigation on the occurrence of Toxoplasma gondii oocysts in cat feces using TOX-element and ITS-1 region targets.

One of the most important routes of transmission for Toxoplasma gondii infection is the ingestion of foods contaminated with cat feces containing sporulated oocysts. The diagnosis of T. gondii infection by fecal microscopy is complicated, as other similar coccidian oocysts are often present in the same fecal specimen. This study aimed to identify T. gondii oocysts in cat feces using a novel PCR technique. Feline fecal specimens (n = 254) were screened for coccidian oocysts by light microscopy using the Sheather's flotation method. PCR analysis performed on the same specimens targeted a 529 bp repeat element and internal transcribed spacer-1 (ITS-1) regions were used to confirm the presence of Toxoplasma oocysts. By light microscopy, 49/254 (19.3%) of specimens contained coccidian oocysts. PCR analysis demonstrated 2/254 (0.8%) and 17/254 (6.7%) positive results using Tox and ITS-1 primers, respectively. However, coccidian oocysts were not identified on microscopic examination of specimens that were PCR-positive by Tox primers. Coccidian oocysts were identified on microscopic examination of 6/17 (35.3%) of the PCR-positive fecal specimens using ITS-1 primers. The BLAST results of 16 ITS-1 sequences were identified as T. gondii (n = 12; 4.7%) and Hammondia hammondi (n = 4; 1.6%). There was slight agreement between the 529 bp and ITS-1 PCR results (κ = 0.148). This is the first report of the detection of Toxoplasma oocysts using PCR analysis on feline fecal specimens from Southern Thailand. The ITS-1 region has potential as an alternative marker to identify T. gondii oocysts in feline fecal specimens.

Impact of seasonal changes on fungal diversity of a semi-arid ecosystem revealed by 454 pyrosequencing.

Fungi play fundamental ecological roles in terrestrial ecosystems. However, their distribution and diversity remain poorly described in natural communities, particularly in arid and semi-arid ecosystems. In order to identify environmental factors determining fungal community structure in these systems, we assessed their diversity in conjunction with soil physicochemical characteristics in a semi-arid ecosystem in Baja California, Mexico, endemic for Coccidioidomycosis (Valley Fever). Two different microhabitats, burrows (influenced by rodent activity) and topsoil, were compared in winter and summer. Using a metagenomic approach, the ITS1 region of nuclear ribosomal DNA was used as barcode. A total of 1940 Operational Taxonomic Units (OTUs) were identified from 362 332 ITS1 sequences obtained by 454 pyrosequencing. Differences in fungal composition between seasons were clearly identified. Moreover, differences in composition between microhabitats were mainly correlated to significant differences in environmental factors, such as moisture and clay content in topsoil samples, and temperature and electrical conductivity in burrow samples. Overall, the fungal community structure (dominated by Ascomycota and Basidiomycota) was less variable between seasons in burrow than in topsoil samples. Coccidioides spp. went undetected by pyrosequencing. However, a nested PCR approach revealed its higher prevalence in burrows.

The Quantification of Representative Sequences pipeline for amplicon sequencing: case study on within-population ITS1 sequence variation in a microparasite infecting Daphnia.

Next generation sequencing (NGS) platforms are replacing traditional molecular biology protocols like cloning and Sanger sequencing. However, accuracy of NGS platforms has rarely been measured when quantifying relative frequencies of genotypes or taxa within populations. Here we developed a new bioinformatic pipeline (QRS) that pools similar sequence variants and estimates their frequencies in NGS data sets from populations or communities. We tested whether the estimated frequency of representative sequences, generated by 454 amplicon sequencing, differs significantly from that obtained by Sanger sequencing of cloned PCR products. This was performed by analysing sequence variation of the highly variable first internal transcribed spacer (ITS1) of the ichthyosporean Caullerya mesnili, a microparasite of cladocerans of the genus Daphnia. This analysis also serves as a case example of the usage of this pipeline to study within-population variation. Additionally, a public Illumina data set was used to validate the pipeline on community-level data. Overall, there was a good correspondence in absolute frequencies of C. mesnili ITS1 sequences obtained from Sanger and 454 platforms. Furthermore, analyses of molecular variance (amova) revealed that population structure of C. mesnili differs across lakes and years independently of the sequencing platform. Our results support not only the usefulness of amplicon sequencing data for studies of within-population structure but also the successful application of the QRS pipeline on Illumina-generated data. The QRS pipeline is freely available together with its documentation under GNU Public Licence version 3 at http://code.google.com/p/quantification-representative-sequences.

Phylogeny and Taxonomy of the Dermatophytes Using Sequence Analysis of the Ribosomal Internal Transcribed Spacer 1 Region / 대한피부과학회지

BACKGROUND: The species of dermatophytes have been identified and classified by morphological and biochemical characterization as well as by mating experiments. But these techniques are either time consuming or lacking specificity. Recently molecular analysis has been introduced to the field of medical mycology. OBJECTIVE: We investigated the phylogeny and taxonomy of the dermatophytes using sequence analysis of the ribosomal internal transcribed spacer 1 (ITS1) region. METHODS: 15 species of dermatophytes (6 strains of T. rubrum, 4 strains of T. mentagrophytes subtypes, M. canis, M. gypseum, E. floccosum, T. verrucosum, and T. tonsurans) were cultured on Sabouraud dextrose broth and their DNA was extracted by bead-beating method. Cloning and sequencing of PCR product was done. RESULTS: The size of specific bands among dermatophytes was 340 bp in ITS1 region. Phylogenetic analysis of sequences revealed that 6 strains of T. rubrum showed genetically identical patterns in intraspecies, but subtypes of T. mentagrophytes were different. The other dermatophytes showed different patterns in interspecies. The following taxonomy were so closely related: granular form of T. mentagrophytes and T. tonsurans; powdery form, persicolor form and downy form of T. mentagrophytes; and M. gypseum and E. floccosum. CONCLUSION: The phylogenetic analysis of ITS1 region provided useful information for classification and understanding the evolution of dermatophytes species.