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1.
Int J Food Microbiol ; 338: 108983, 2021 Jan 02.
Artigo em Inglês | MEDLINE | ID: mdl-33261862

RESUMO

Microbial ecology is an integral part of an agricultural ecosystem and influences the quality of agricultural commodities. Microbial activity influences grapevine health and crop production, conversion of sugar to ethanol during fermentation, thus forming wine aroma and flavour. There are regionally differentiated microbial patterns in grapevines and must but how microbial patterns contribute to wine regional distinctiveness (terroir) at small scale (<100 km) is not well defined. Here we characterise fungal communities, yeast populations, and Saccharomyces cerevisiae populations during spontaneous fermentation using metagenomics and population genetics to investigate microbial distribution and fungal contributions to the resultant wine. We found differentiation of fungi, yeasts, and S. cerevisiae between geographic origins (estate/vineyard), with influences from the grape variety. Growth and dominance of S. cerevisiae during fermentation reshaped the fungal community and showed geographic structure at the strain level. Associations between fungal microbiota diversity and wine chemicals suggest that S. cerevisiae plays a primary role in determining wine aroma profiles at a sub-regional scale. The geographic distribution at scales of less than 12 km supports that differential microbial communities, including the dominant fermentative yeast S. cerevisiae can be distinct in a local setting. These findings provide further evidence for microbial contributions to wine terroir, and perspectives for sustainable agricultural practices to maintain microbial diversity and optimise fermentation function to craft beverage quality.


Assuntos
Biodiversidade , Fermentação , Fungos/classificação , Microbiota , Vinho/microbiologia , Agricultura , Fazendas , Fungos/química , Fungos/metabolismo , Odorantes , Saccharomyces cerevisiae , Vitis/microbiologia
2.
J Appl Microbiol ; 130(1): 109-122, 2021 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-32619072

RESUMO

AIMS: The soil microbial community plays a critical role in increasing phosphorus (P) availability in low-P, weathered soils by "mining" recalcitrant organic P through the production of phosphatase enzymes. However, there is a lack of data on the fungal and bacterial taxa which are directly involved in P mining, which could also serve as potential microbial bioindicators of low P availability. METHODS AND RESULTS: Leveraging a 5-year P enrichment experiment on low-P forest soils, high-throughput sequencing was used to profile the microbial community to determine which taxa associate closely with P availability. We hypothesized that there would be a specialized group of soil micro-organisms that could access recalcitrant P and whose presence could serve as a bioindicator of P mining. Community profiling revealed several candidate bioindicators of P mining (Russulales, Acidobacteria Subgroup 2, Acidobacteriales, Obscuribacterales and Solibacterales), whose relative abundance declined with elevated P and had a significant, positive association with phosphatase production. In addition, we identified candidate bioindicators of high P availability (Mytilinidales, Sebacinales, Chitinophagales, Cytophagales, Saccharimonadales, Opitulales and Gemmatales). CONCLUSIONS: This research provides evidence that mitigating P limitation in this ecosystem may be a specialized trait and is mediated by a few microbial taxa. SIGNIFICANCE AND IMPACT OF THE STUDY: Here, we characterize Orders of soil microbes associated with manipulated phosphorus availability in forest soils to determine bioindicator candidates for phosphorus. Likewise, we provide evidence that the microbial trait to utilize recalcitrant organic forms of P (e.g. P mining) is likely a specialized trait and not common to all members of the soil microbial community. This work further elucidates the role that a complex microbial community plays in the cycling of P in low-P soils, and provides evidence for future studies on microbial linkages to human-induced ecosystem changes.


Assuntos
Biomarcadores Ambientais , Florestas , Microbiota , Fósforo/metabolismo , Microbiologia do Solo , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Bactérias/metabolismo , Fungos/classificação , Fungos/genética , Fungos/isolamento & purificação , Fungos/metabolismo , Humanos , Microbiota/genética , Monoéster Fosfórico Hidrolases/análise , Monoéster Fosfórico Hidrolases/metabolismo , Fósforo/análise , Solo/química
3.
J Appl Microbiol ; 130(1): 179-195, 2021 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-32590882

RESUMO

AIMS: Sustainable agriculture requires effective and safe biofertilizers and biofungicides with low environmental impact. Natural ecosystems that closely resemble the conditions of biosaline agriculture may present a reservoir for fungal strains that can be used as novel bioeffectors. METHODS AND RESULTS: We isolated a library of fungi from the rhizosphere of three natural halotolerant plants grown in the emerging tidal salt marshes on the south-east coast of China. DNA barcoding of 116 isolates based on the rRNA ITS1 and 2 and other markers (tef1 or rpb2) revealed 38 fungal species, including plant pathogenic (41%), saprotrophic (24%) and mycoparasitic (28%) taxa. The mycoparasitic fungi were mainly species from the hypocrealean genus Trichoderma, including at least four novel phylotypes. Two of them, representing the taxa Trichoderma arenarium sp. nov. (described here) and T. asperelloides, showed antagonistic activity against five phytopathogenic fungi, and significant growth promotion on tomato seedlings under the conditions of saline agriculture. CONCLUSIONS: Trichoderma spp. of salt marshes play the role of natural biological control in young soil ecosystems with a putatively premature microbiome. SIGNIFICANCE AND IMPACT OF THE STUDY: The saline soil microbiome is a rich source of halotolerant bioeffectors that can be used in biosaline agriculture.


Assuntos
Agricultura/métodos , Águas Salinas , Trichoderma/fisiologia , Áreas Alagadas , Antibiose , China , Fungos/classificação , Fungos/genética , Fungos/metabolismo , Lycopersicon esculentum/crescimento & desenvolvimento , Lycopersicon esculentum/microbiologia , Rizosfera , Plântula/crescimento & desenvolvimento , Plântula/microbiologia , Microbiologia do Solo , Trichoderma/classificação , Trichoderma/genética , Trichoderma/metabolismo
4.
Can J Microbiol ; 67(1): 29-36, 2021 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-32780963

RESUMO

Plant fungal endophytes are diverse microbial sources that reside inside plants. Grapes (Vitis vinifera) are rich in polyphenols that have beneficial health effects, and recent research has shown that fungal endophytes in grapes may contribute to the production of these polyphenols and may serve as biocontrol agents. In this study, we determined the fungal microbial endophyte diversity in North American table grapes found at a Winnipeg, Manitoba, market. The amplicon internal transcribed spacer (ITS) metagenomics approach was used to profile the fungal communities of the fruit endophyte microbiome of three table grape types. The data supported endophyte diversity in different table grapes, including possible bioactive, saprophytic, and pathogenic fungi. Culturable endophytes were isolated and identified by morphology and ITS amplicon sequencing. The majority of the isolated culturable strains included Alternaria spp. and Cladosporium spp. The results provided evidence of the existence of diverse fungal endophytes isolated and identified from the fruit of the table grapes. These fungal endophytes may have potential in agricultural, industrial, and pharmaceutical applications.


Assuntos
Endófitos/isolamento & purificação , Fungos/isolamento & purificação , Vitis/microbiologia , Biodiversidade , DNA Espaçador Ribossômico/genética , Endófitos/classificação , Endófitos/genética , Frutas/microbiologia , Fungos/classificação , Fungos/genética , Manitoba , Microbiota/genética
5.
BMC Evol Biol ; 20(1): 163, 2020 12 09.
Artigo em Inglês | MEDLINE | ID: mdl-33297950

RESUMO

BACKGROUND: Monoculture farming poses significant disease challenges, but fungus-farming termites are able to successfully keep their monoculture crop free from contamination by other fungi. It has been hypothesised that obligate gut passage of all plant substrate used to manure the fungal symbiont is key to accomplish this. Here we refute this hypothesis in the fungus-farming termite species Macrotermes bellicosus. RESULTS: We first used ITS amplicon sequencing to show that plant substrate foraged on by termite workers harbour diverse fungal communities, which potentially could challenge the farming symbiosis. Subsequently, we cultivated fungi from dissected sections of termite guts to show that fungal diversity does not decrease during gut passage. Therefore, we investigated if healthy combs harboured these undesirable fungal genera, and whether the presence of workers affected fungal diversity within combs. Removal of workers led to a surge in fungal diversity in combs, implying that termite defences must be responsible for the near-complete absence of other fungi in functioning termite gardens. CONCLUSIONS: The rapid proliferation of some of these fungi when colonies are compromised indicates that some antagonists successfully employ a sit-and-wait strategy that allows them to remain dormant until conditions are favourable. Although this strategy requires potentially many years of waiting, it prevents these fungi from engaging in an evolutionary arms race with the termite host, which employs a series of complementary behavioural and chemical defences that may prove insurmountable.


Assuntos
Biodiversidade , Fungos , Microbioma Gastrointestinal , Isópteros , Animais , DNA Intergênico/genética , Fungos/classificação , Fungos/genética , Isópteros/microbiologia , Filogenia , Simbiose
6.
Nat Commun ; 11(1): 6096, 2020 11 30.
Artigo em Inglês | MEDLINE | ID: mdl-33257660

RESUMO

Phylogenetic trees are essential for studying biology, but their reproducibility under identical parameter settings remains unexplored. Here, we find that 3515 (18.11%) IQ-TREE-inferred and 1813 (9.34%) RAxML-NG-inferred maximum likelihood (ML) gene trees are topologically irreproducible when executing two replicates (Run1 and Run2) for each of 19,414 gene alignments in 15 animal, plant, and fungal phylogenomic datasets. Notably, coalescent-based ASTRAL species phylogenies inferred from Run1 and Run2 sets of individual gene trees are topologically irreproducible for 9/15 phylogenomic datasets, whereas concatenation-based phylogenies inferred twice from the same supermatrix are reproducible. Our simulations further show that irreproducible phylogenies are more likely to be incorrect than reproducible phylogenies. These results suggest that a considerable fraction of single-gene ML trees may be irreproducible. Increasing reproducibility in ML inference will benefit from providing analyses' log files, which contain typically reported parameters (e.g., program, substitution model, number of tree searches) but also typically unreported ones (e.g., random starting seed number, number of threads, processor type).


Assuntos
Filogenia , Reprodutibilidade dos Testes , Animais , Fungos/classificação , Fungos/genética , Genes/genética , Funções Verossimilhança , Mamíferos/genética , Modelos Genéticos , Modelos Estatísticos , Plantas/classificação , Plantas/genética
7.
PLoS One ; 15(11): e0242258, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33211760

RESUMO

Endophytic fungi play an important role in plant growth. The composition and structure of endophytes vary in different plant tissues, which are specific habitats for endophyte colonization. To analyze the diversity and structural composition of endophytic fungi from toothed clubmoss (Huperzia serrata) that was artificially cultivated for 3 years, we investigated endophytic fungi from the roots, stems and leaves using comparative sequence analysis of the ITS2 region of the fungal rRNA genes sequenced with high-throughput sequencing technology. Seven fungal phyla were identified, and fungal diversity and structure varied across different tissues, with the most distinctive community features found in the roots. A total of 555 operational taxonomic units (OTUs) were detected, and 198 were common to all samples, and 43, 16, 16 OTUs were unique to the root, stem, leaf samples, respectively. Taxonomic classification showed that Ascomycota and Basidiomycota were dominant phyla, and Cladosporium, Oidiodendron, Phyllosticta, Sebacina and Ilyonectria were dominant genera. The relative abundance heat map at the genus level suggested that H. serrata had characteristic endophytic fungal microbiomes. Line discriminant analysis effect size analysis and principal coordinate analysis demonstrated that fungal communities were tissue-type and tissue-site specific. Overall, our study provides new insights into the complex composition of endophytic fungi in H. serrata.


Assuntos
Fungos/genética , Huperzia/microbiologia , Ascomicetos/classificação , Ascomicetos/genética , Ascomicetos/isolamento & purificação , Basidiomycota/classificação , Basidiomycota/genética , Basidiomycota/isolamento & purificação , Fungos/classificação , Fungos/isolamento & purificação , Sequenciamento de Nucleotídeos em Larga Escala , Filogenia , Folhas de Planta/microbiologia , Raízes de Plantas/microbiologia , Caules de Planta/microbiologia , Análise de Componente Principal , RNA Ribossômico/química , RNA Ribossômico/genética , RNA Ribossômico/metabolismo , Análise de Sequência de DNA
8.
PLoS One ; 15(11): e0241283, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33151966

RESUMO

Kuwait is a country with a very high dust loading; in fact it bears the world's highest particulate matter concentration in the outdoor air. The airborne dust often has associated biological materials, including pathogenic microbes that pose a serious risk to the urban ecosystem and public health. This study has established the baseline taxonomic characterization of microbes associated with dust transported into Kuwait from different trajectories. A high volume air sampler with six-stage cascade impactor was deployed for sample collection at a remote as well as an urban site. Samples from three different seasons (autumn, spring and summer) were subjected to targeted amplicon sequencing. A set of ~ 50 and 60 bacterial and fungal genera, respectively, established the core air microbiome. The predominant bacterial genera (relative abundance ≥ 1%) were Brevundimonas (12.5%), Sphingobium (3.3%), Sphingopyxis (2.7%), Pseudomonas (2.5%), Sphingomonas (2.4%), Massilia (2.3%), Acidovorax (2.0%), Allorhizobium (1.8%), Halomonas (1.3%), and Mesorhizobium (1.1%), and the fungal taxa were Cryptococcus (12%) followed by Alternaria (9%), Aspergillus (7%), Candida (3%), Cladosporium (2.9%), Schizophyllum (1.6%), Fusarium (1.4%), Gleotinia (1.3%) and Penicillium (1.15%). Significant spatio-temporal variations were recorded in terms of relative abundances, α-diversities, and ß-diversities of bacterial communities. The dissimilarities were less pronounced and instead the communities were fairly homogenous. Linear discrimant analysis revealed three fungal genera known to be significantly differentially abundant with respect to different size fractions of dust. Our results shed light on the spatio-temporal distribution of airborne microbes and their implications in general health.


Assuntos
Aerossóis/análise , Bactérias/isolamento & purificação , Poeira/análise , Fungos/isolamento & purificação , Análise Espaço-Temporal , Bactérias/classificação , Biodiversidade , Análise por Conglomerados , Análise Discriminante , Fungos/classificação , Kuweit , Microbiota , Análise de Componente Principal , Estações do Ano
9.
Mem Inst Oswaldo Cruz ; 115: e200430, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33053052

RESUMO

Despite the medical advances and interventions to improve the quality of life of those in intensive care, people with cancer or severely immunocompromised or other susceptible hosts, invasive fungal diseases (IFD) remain severe and underappreciated causes of illness and death worldwide. Therefore, IFD continue to be a public health threat and a major hindrance to the success of otherwise life-saving treatments and procedures. Globally, hundreds of thousands of people are affected every year with Candida albicans, Aspergillus fumigatus, Cryptococcus neoformans, Pneumocystis jirovecii, endemic dimorphic fungi and Mucormycetes, the most common fungal species causing invasive diseases in humans. These infections result in morbidity and mortality rates that are unacceptable and represent a considerable socioeconomic burden. Raising the general awareness of the significance and impact of IFD in human health, in both the hospital and the community, is hence critical to understand the scale of the problem and to raise interest to help fighting these devastating diseases.


Assuntos
Fungos , Infecções Fúngicas Invasivas/diagnóstico , Efeitos Psicossociais da Doença , Fungos/classificação , Fungos/isolamento & purificação , Humanos , Hospedeiro Imunocomprometido , Unidades de Terapia Intensiva , Infecções Fúngicas Invasivas/complicações , Infecções Fúngicas Invasivas/mortalidade , Qualidade de Vida
10.
Nat Commun ; 11(1): 5125, 2020 10 12.
Artigo em Inglês | MEDLINE | ID: mdl-33046698

RESUMO

Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucoromycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present a combined analysis of 135 fungal genomes from 73 saprotrophic, endophytic and pathogenic species, and 62 mycorrhizal species, including 29 new mycorrhizal genomes. This study samples ecologically dominant fungal guilds for which there were previously no symbiotic genomes available, including ectomycorrhizal Russulales, Thelephorales and Cantharellales. Our analyses show that transitions from saprotrophy to symbiosis involve (1) widespread losses of degrading enzymes acting on lignin and cellulose, (2) co-option of genes present in saprotrophic ancestors to fulfill new symbiotic functions, (3) diversification of novel, lineage-specific symbiosis-induced genes, (4) proliferation of transposable elements and (5) divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.


Assuntos
Fungos/genética , Genoma Fúngico , Micorrizas/genética , Simbiose , Ecossistema , Evolução Molecular , Proteínas Fúngicas/genética , Fungos/classificação , Fungos/fisiologia , Micorrizas/classificação , Micorrizas/fisiologia , Filogenia , Fenômenos Fisiológicos Vegetais , Plantas/microbiologia
11.
Int J Food Microbiol ; 335: 108889, 2020 Dec 16.
Artigo em Inglês | MEDLINE | ID: mdl-33007604

RESUMO

The safety and quality of cereal grain supplies are adversely impacted by microbiological contamination, with novel interventions required to maximise whole grains safety and stability. The microbiological contaminants of wheat grains and the efficacy of Atmospheric Cold Plasma (ACP) for potential to control these risks were investigated. The evaluations were performed using a contained reactor dielectric barrier discharge (DBD) system; samples were treated for 0-20 min using direct and indirect plasma exposure. Amplicon-based metagenomic analysis using bacterial 16S rRNA gene and fungal 18S rRNA gene with internal transcribed spacer (ITS) region was performed to characterize the change in microbial community composition in response to ACP treatment. The antimicrobial efficacy of ACP against a range of bacterial and fungal contaminants of wheat, was assessed to include individual isolates from grains as challenge pathogens. ACP influenced wheat microbiome composition, with a higher microbial diversity as well as abundance found on the untreated control grain samples. Culture and genomic approaches revealed different trends for mycoflora detection and control. A challenge study demonstrated that using direct mode of plasma exposure with 20 min of treatment significantly reduced the concentration of all pathogens. Overall, reduction levels for B. atrophaeus vegetative cells were higher than for all fungal species tested, whereas B. atrophaeus spores were the most resistant to ACP among all microorganisms tested. Of note, repeating sub-lethal plasma treatment did not induce resistance to ACP in either B. atrophaeus or A. flavus spores. ACP process control could be tailored to address diverse microbiological risks for grain stability and safety.


Assuntos
Anti-Infecciosos/farmacologia , Resistência Microbiana a Medicamentos , Microbiota/efeitos dos fármacos , Gases em Plasma/farmacologia , Triticum/microbiologia , Bactérias/classificação , Bactérias/efeitos dos fármacos , Bactérias/genética , Bactérias/isolamento & purificação , Grão Comestível/microbiologia , Fungos/classificação , Fungos/efeitos dos fármacos , Fungos/genética , Fungos/isolamento & purificação , RNA Ribossômico/genética , Especificidade da Espécie
12.
Lett Appl Microbiol ; 71(6): 667-678, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-32869331

RESUMO

Microbial diversity of pit mud (PM) plays a significant role in Baijiu's flavour. Here we explored the microbial community structures and aroma substances of Wenwang Winery with high-throughput sequencing coupling with headspace solid-phase microextraction-gas chromatography-mass spectrometry. We discovered that the odorant was mainly derived from 14 aroma compounds because of their OAVs ≥ 1 (OAV, the ratio of substance concentration to aroma threshold; s, on behalf of the plural), such as ethyl hexanoate (2438), ethyl octanoate (975), caproic acid (52) and etc. Moreover we also revealed that Lactobacillaceae (97·08%) was the mainly bacterial microbial community in 2-year-old PM, companied by the primarily fungi including Aspergillaceae (55·45%), Unclassified Ascomycota (11·13%) and Dipodascaceae (5·72%). Compared with the 2-year-old PM, bacterial floras in 20-year-old PM and 30-year-old PM were more abundant (i.e. Dysgonomonadaceae, Clostridium and Synerggstaceas), while no fungi were detected. Besides, the physicochemical analysis showed that the content of Lactobacillaceae was inversely associated with moisture, pH and ammonia nitrogen. By further Spearman's correlation coefficient analysis, we verified that the content of Lactobacillaceae was positively correlated with ethyl hexanoate, while negatively correlated with ethyl octanoate and caproic acid. Meanwhile, ethyl octanoate and caproic acid were positively correlated with most flora including Ruminococcaceae, Dysgonomonadaceae and Clostridiacea, which were related to physicochemical indexes. This work demonstrates promise for adjusting the physicochemical indexes of PM to affect the micro-organisms and aroma, which may provide a reference for the production of high-quality Baijiu.


Assuntos
Bactérias/isolamento & purificação , Biodiversidade , Odorantes/análise , Microbiologia do Solo , Solo/química , Bactérias/classificação , Bactérias/genética , Bactérias/metabolismo , Fungos/classificação , Fungos/genética , Fungos/isolamento & purificação , Fungos/metabolismo , Cromatografia Gasosa-Espectrometria de Massas/métodos , Microbiota , Microextração em Fase Sólida
13.
Extremophiles ; 24(6): 821-829, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32974723

RESUMO

Fungi are widely distributed in all terrestrial ecosystems, and they are essential to the recycling of nutrients in all terrestrial habitats on earth. We wanted to determine the relationship between soil fungal communities and geochemical factors (geographical location and soil physicochemical properties) in three widely separated geographical regions (the Antarctic, Arctic, and Tibet Plateau). Using high-throughput Illumina amplicon sequencing, we characterized the fungal communities in 53 soil samples collected from the three regions. The fungal richness and diversity indices were not significantly different among the three regions. However, fungal community composition and many fungal taxa (Thelebolales, Verrucariales, Sordariales, Chaetothyriales, Hypocreales, Pleosporales, Capnodiales, and Dothideales) significantly differed among three regions. Furthermore, geographical location (latitude and altitude) and six soil physicochemical properties (SiO42--Si, pH, NO3--N, organic nitrogen, NO2--N, and organic carbon) were significant geochemical factors those were correlated with the soil fungal community composition. These results suggest that many geochemical factors influence the distribution of the fungal species within the Antarctic, Arctic, and Tibet Plateau.


Assuntos
Fungos/classificação , Micobioma , Microbiologia do Solo , Regiões Antárticas , Regiões Árticas , Ecossistema , Tibet
14.
Int J Food Microbiol ; 334: 108833, 2020 Dec 02.
Artigo em Inglês | MEDLINE | ID: mdl-32911159

RESUMO

This work aims to provide the first study on the mycobiota present in Chilean pepper Capsicum annuum L. cv. "Cacho de Cabra" throughout the early production stages. Two hundred and forty berry fruits were sampled: 1) at the ripe fruits harvest day; 2) during drying; and 3) smoking processes. A total of 192 strains, encompassing 11 genera and 44 species, were identified through analysis of ß-tubulin (benA) gene and internal transcribed spacer of ribosomal DNA (ITS) region. All collection points showed samples with high fungal contamination, but the mycobiota composition varied as a result of different environmental conditions. Alternaria spp. and Fusarium spp. were predominantly isolated from fresh fruits of C. annuum. Penicillium spp. was the most frequent genus in all analysed points. Penicillium brevicompactum and P. crustosum were the most abundant species. Among Aspergillus, A. niger and A. flavus were dominant after the drying phase. In our study, none of the analysed strains of Penicillium (113) and Aspergillus (35) produced Ochratoxin A at detectable levels. The broad characterization of the fungal community of C. annuum carried out in this study, could be a guideline for future mycotoxin analyses performed directly on the pod. Understanding the role and dynamics of mycobiota and its relationship with the toxins present in this substrate, will be useful to establish and improve control measures considering the specificities of each point in the C. annuum production chain.


Assuntos
Capsicum/microbiologia , Microbiologia de Alimentos/métodos , Alimentos em Conserva/microbiologia , Micobioma , Chile , DNA Espaçador Ribossômico/genética , Frutas/microbiologia , Fungos/classificação , Fungos/genética , Fungos/isolamento & purificação , Micotoxinas/análise , Tubulina (Proteína)/genética
15.
Sci Rep ; 10(1): 15115, 2020 09 15.
Artigo em Inglês | MEDLINE | ID: mdl-32934253

RESUMO

Pulque is a culturally important 4,000-year-old traditional Mexican fermented drink. Pulque is produced by adding fresh aguamiel (agave sap) to mature pulque, resulting in a mixture of microbial communities and chemical compositions. We performed shotgun metagenomic sequencing of five stages of pulque fermentation to characterize organismal and functional diversity. We identified 6 genera (Acinetobacter, Lactobacillus, Lactococcus, Leuconostoc, Saccharomyces and Zymomonas) and 10 species (Acinetobacter boissieri, Acinetobacter nectaris, Lactobacillus sanfranciscensis, Lactococcus lactis, Lactococcus piscium, Lactococcus plantarum, Leuconostoc citreum, Leuconostoc gelidum, Zymomonas mobilis and Saccharomyces cerevisiae) that were present ≥ 1% in at least one stage of pulque fermentation. The abundance of genera and species changed during fermentation and was associated with a decrease in sucrose and increases in ethanol and lactic acid, suggesting that resource competition shapes organismal diversity. We also predicted functional profiles, based on organismal gene content, for each fermentation stage and identified an abundance of genes associated with the biosynthesis of folate, an essential B-vitamin. Additionally, we investigated the evolutionary relationships of S. cerevisiae and Z. mobilis, two of the major microbial species found in pulque. For S. cerevisiae, we used a metagenomics assembly approach to identify S. cerevisiae scaffolds from pulque, and performed phylogenetic analysis of these sequences along with a collection of 158 S. cerevisiae strains. This analysis suggests that S. cerevisiae from pulque is most closely related to Asian strains isolated from sake and bioethanol. Lastly, we isolated and sequenced the whole-genomes of three strains of Z. mobilis from pulque and compared their relationship to seven previously sequenced isolates. Our results suggest pulque strains may represent a distinct lineage of Z. mobilis.


Assuntos
Agave/microbiologia , Bebidas Alcoólicas/microbiologia , Bactérias/genética , DNA Bacteriano/análise , DNA Fúngico/análise , Fungos/genética , Metagenoma , Bactérias/classificação , Bactérias/metabolismo , Fermentação , Fungos/classificação , Fungos/metabolismo
16.
Nat Commun ; 11(1): 4721, 2020 09 18.
Artigo em Inglês | MEDLINE | ID: mdl-32948775

RESUMO

The importance of soil age as an ecosystem driver across biomes remains largely unresolved. By combining a cross-biome global field survey, including data for 32 soil, plant, and microbial properties in 16 soil chronosequences, with a global meta-analysis, we show that soil age is a significant ecosystem driver, but only accounts for a relatively small proportion of the cross-biome variation in multiple ecosystem properties. Parent material, climate, vegetation and topography predict, collectively, 24 times more variation in ecosystem properties than soil age alone. Soil age is an important local-scale ecosystem driver; however, environmental context, rather than soil age, determines the rates and trajectories of ecosystem development in structure and function across biomes. Our work provides insights into the natural history of terrestrial ecosystems. We propose that, regardless of soil age, changes in the environmental context, such as those associated with global climatic and land-use changes, will have important long-term impacts on the structure and function of terrestrial ecosystems across biomes.


Assuntos
Biota , Ecossistema , Solo/química , Bactérias/classificação , Biodiversidade , Biomassa , Clima , Fungos/classificação , Microbiota , Plantas/classificação , Fatores de Tempo
17.
Sci Rep ; 10(1): 13685, 2020 08 13.
Artigo em Inglês | MEDLINE | ID: mdl-32792547

RESUMO

Fungal endophytes can influence production and post-harvest challenges in carrot, though the identity of these microbes as well as factors affecting their composition have not yet been determined, which prevents growers from managing these organisms to improve crop performance. Consequently, we characterized the endophytic mycobiome in the taproots of three carrot genotypes that vary in resistance to two pathogens grown in a trial comparing organic and conventional crop management using Illumina sequencing of the internal transcribed spacer (ITS) gene. A total of 1,480 individual operational taxonomic units (OTUs) were identified. Most were consistent across samples, indicating that they are part of a core mycobiome, though crop management influenced richness and diversity, likely in response to differences in soil properties. There were also differences in individual OTUs among genotypes and the nematode resistant genotype was most responsive to management system indicating that it has greater control over its endophytic mycobiome, which could potentially play a role in resistance. Members of the Ascomycota were most dominant, though the exact function of most taxa remains unclear. Future studies aimed at overcoming difficulties associated with isolating fungal endophytes are needed to identify these microbes at the species level and elucidate their specific functional roles.


Assuntos
Daucus carota/crescimento & desenvolvimento , Fungos/classificação , Análise de Sequência de DNA/métodos , Agricultura , Daucus carota/genética , Daucus carota/microbiologia , Endófitos , Fungos/genética , Genótipo , Sequenciamento de Nucleotídeos em Larga Escala , Micobioma , Filogenia , Raízes de Plantas/microbiologia
18.
PLoS One ; 15(8): e0238149, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32833991

RESUMO

As a characteristic edible fungus with a high nutritional value and medicinal effect, the Bachu mushroom has a broad market. To distinguish among Bachu mushrooms with high value and other fungi effectively and accurately, as well as to explore a universal identification method, this study proposed a method to identify Bachu mushrooms by Fourier Transform Infrared Spectroscopy (FT-IR) combined with machine learning. In this experiment, two kinds of common edible mushrooms, Lentinus edodes and club fungi, were selected and classified with Bachu mushrooms. Due to the different distribution of nutrients in the caps and stalks, the caps and stalks were studied in this experiment. By comparing the average normalized infrared spectra of the caps and stalks of the three types of fungi, we found differences in their infrared spectra, indicating that the latter can be used to classify and identify the three types of fungi. We also used machine learning to process the spectral data. The overall steps of data processing are as follows: use partial least squares (PLS) to extract spectral features, select the appropriate characteristic number, use different classification algorithms for classification, and finally determine the best algorithm according to the classification results. Among them, the basis of selecting the characteristic number was the cumulative variance interpretation rate. To improve the reliability of the experimental results, this study also used the classification results to verify the feasibility. The classification algorithms used in this study were the support vector machine (SVM), backpropagation neural network (BPNN) and k-nearest neighbors (KNN) algorithm. The results showed that the three algorithms achieved good results in the multivariate classification of the caps and stalks data. Moreover, the cumulative variance explanation rate could be used to select the characteristic number. Finally, by comparing the classification results of the three algorithms, the classification effect of KNN was found to be the best. Additionally, the classification results were as follows: according to the caps data classification, the accuracy was 99.06%; according to the stalks data classification, the accuracy was 99.82%. This study showed that infrared spectroscopy combined with a machine learning algorithm has the potential to be applied to identify Bachu mushrooms and the cumulative variance explanation rate can be used to select the characteristic number. This method can also be used to identify other types of edible fungi and has a broad application prospect.


Assuntos
Agaricales/classificação , Espectroscopia de Infravermelho com Transformada de Fourier/métodos , Algoritmos , Confiabilidade dos Dados , Análise Discriminante , Fungos/classificação , Análise dos Mínimos Quadrados , Aprendizado de Máquina , Redes Neurais de Computação , Análise de Componente Principal/métodos , Reprodutibilidade dos Testes , Cogumelos Shiitake , Espectrofotometria Infravermelho/métodos , Máquina de Vetores de Suporte
19.
J Environ Public Health ; 2020: 4609164, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32733576

RESUMO

Air pollution has been a major challenge worldwide particularly in the developing world. Improper waste disposal and management may result in microbial air pollution. In advanced countries, landfill sites are far from neighborhoods; however, the opposite is observed for landfill sites in the developing world. In Accra, some landfill sites are 100 meters from neighborhoods. The aim of this study was to assess the microbial air quality and associated environmental health hazards of landfill sites in selected districts in the Greater Accra Region of Ghana. A random sampling method was employed to select sampling sites across the dry and wet seasons from landfills and their corresponding neighborhoods. Results obtained showed a higher total count (CFU/m3) of bacteria and fungi in the air at the landfill sites than neighborhoods. Statistically significant variation (p < 0.05) in bacterial and fungal concentrations over two seasons was found for both landfills and neighborhoods. However, bacterial concentrations were significantly higher than fungal concentrations (p < 0.05) across seasons for all locations. Staphylococcus epidermidis was the highest (15.6 %) occurring microbe at both landfill sites and neighborhoods. This was followed by Staphylococcus aureus (12.7%). Other bacteria and fungi of public health importance such as Pseudomonas aeruginosa, Escherichia coli, Aspergillus flavus, and Aspergillus niger were also isolated from the study sites, above the WHO recommended levels. In conclusion, the landfill waste disposal and its close proximity to neighborhoods as observed in this study pose a potential environmental health risk, with dire implications for public health and safety. The government must enact and implement policies to regulate waste management and to ensure public safety.


Assuntos
Microbiologia do Ar , Poluentes Atmosféricos/análise , Instalações de Eliminação de Resíduos , Poluentes Atmosféricos/normas , Bactérias/classificação , Bactérias/isolamento & purificação , Monitoramento Ambiental , Fungos/classificação , Fungos/isolamento & purificação , Gana , Saúde Pública , Eliminação de Resíduos , Medição de Risco
20.
Int J Food Microbiol ; 334: 108806, 2020 Dec 02.
Artigo em Inglês | MEDLINE | ID: mdl-32805512

RESUMO

Due to its chemical properties, honey does not foster the growth of microorganisms, however it may contain a rich microbial community, including viable, stressed, and not viable microbes. In order to characterize honey microbiota focusing on the difference between products from beekeepers and large retail in the present study a culture-independent approach based on DNA metabarcoding was applied. Honey samples were collected from Local Beekeepers (LB) and Market sales (M) during four years with the aim to investigate the microbiological quality in the honey market. Extraction and amplification of DNA from honey samples showed reduced efficiency with increasing age of honey, with the loss of 50-80% of samples four years old (2014). For this reason, only samples of similar age were compared and the analysis of microbial communities focused on year 2017, for a total of 75 samples. Differences in alpha and beta-diversity were evidenced comparing microbial communities between LB and M samples. In particular, contaminant bacteria dominated the microbiota in M samples while LB samples were enriched in Lactic Acid Bacteria (LAB) that cannot be isolated with culture-dependent approaches.


Assuntos
Bactérias/isolamento & purificação , Fungos/isolamento & purificação , Mel/microbiologia , Microbiota , Bactérias/classificação , Bactérias/genética , Código de Barras de DNA Taxonômico , DNA Bacteriano/genética , DNA Fúngico/genética , Microbiologia de Alimentos , Fungos/classificação , Fungos/genética , Itália , Lactobacillales/classificação , Lactobacillales/genética , Lactobacillales/isolamento & purificação , Microbiota/genética
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