scholarly journals A culture‐independent approach to understanding the role of soil fungal communities in Bromus tectorum stand failure

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Nathan J. Ricks ◽  
Taryn Williamson ◽  
Susan E. Meyer ◽  
John M. Chaston ◽  
Craig E. Coleman
Keyword(s):  
Bromus Tectorum ◽  
Fungal Communities ◽  
Culture Independent

scholarly journals A Culture-independent Approach to Understanding the Role of Soil Fungal Communities in Bromus tectorum Stand Failure

2020 ◽  
Author(s):  
Nathan Ricks ◽  
Taryn Williamson ◽  
Susan Meyer ◽  
John Chaston ◽  
Craig Coleman
Keyword(s):  
Bromus Tectorum ◽  
Fungal Communities ◽  
Culture Independent

Diversity of endolithic fungal communities in dolomite and limestone rocks from Nanjiang Canyon in Guizhou karst area, China

2012 ◽  
Vol 58 (6) ◽  
pp. 685-693 ◽  
Author(s):  
Yuan Tang ◽  
Bin Lian
Keyword(s):  
Carbonate Rocks ◽  
Fungal Communities ◽  
Karst Area ◽  
Low Frequencies ◽  
Rock Samples ◽  
Rock Fragments ◽  
Culture Independent ◽  
Rapid Temperature ◽  
Common Genus

The endolithic environment, the tiny pores and cracks in rocks, buffer microbial communities from a number of physical stresses, such as desiccation, rapid temperature variations, and UV radiation. Considerable knowledge has been acquired about the diversity of microorganisms in these ecosystems, but few culture-independent studies have been carried out on the diversity of fungi to date. Scanning electron microscopy of carbonate rock fragments has revealed that the rock samples contain certain kinds of filamentous fungi. We evaluated endolithic fungal communities from bare dolomite and limestone rocks collected from Nanjiang Canyon (a typical karst canyon in China) using culture-independent methods. Results showed that Ascomycota was absolutely dominant both in the dolomite and limestone fungal clone libraries. Basidiomycota and other eukaryotic groups (Bryophyta and Chlorophyta) were only detected occasionally or at low frequencies. The most common genus in the investigated carbonate rocks was Verrucaria. Some other lichen-forming fungi (e.g., Caloplaca , Exophiala , and Botryolepraria ), Aspergillus , and Penicillium were also identified from the rock samples. The results provide a cross-section of the endolithic fungal communities in carbonate rocks and help us understand more about the role of microbes (fungi and other rock-inhabiting microorganisms) in rock weathering and pedogenesis.

scholarly journals Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota

2017 ◽  
Author(s):  
Sean M. Kearney ◽  
Sean M. Gibbons ◽  
Mathilde Poyet ◽  
Thomas Gurry ◽  
Kevin Bullock ◽  
...  
Keyword(s):  
Dietary Fatty Acids ◽  
Resistant Bacteria ◽  
Human Gut ◽  
Environmental Signals ◽  
Human Microbiota ◽  
Disease States ◽  
Culture Independent ◽  
Health And Disease ◽  
Over Time

AbstractEndospore-formers in the human microbiota are well adapted for host-to-host transmission, and an emerging consensus points to their role in determining health and disease states in the gut. The human gut, more than any other environment, encourages the maintenance of endospore formation, with recent culture-based work suggesting that over 50% of genera in the microbiome carry genes attributed to this trait. However, there has been limited work on the ecological role of endospores and other stress-resistant cellular states in the human gut. In fact, there is no data to indicate whether organisms with the genetic potential to form endospores actually form endosporesin situand how sporulation varies across individuals and over time. Here, we applied a culture-independent protocol to enrich for endospores and other stress-resistant cells in human feces to identify variation in these states across people and within an individual over time. We see that cells with resistant states are more likely than those without to be shared among multiple individuals, which suggests that these resistant states are particularly adapted for cross-host dissemination. Furthermore, we use untargeted fecal metabolomics in 24 individuals and within a person over time to show that these organisms respond to shared environmental signals, and in particular, dietary fatty acids, that likely mediate colonization of recently disturbed human guts.

scholarly journals The Mycobiota of the Deep Sea: What Omics Can Offer

Life ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 292
Author(s):  
Lluvia Vargas-Gastélum ◽  
Meritxell Riquelme
Keyword(s):  
Deep Sea ◽  
Fungal Diversity ◽  
High Salinity ◽  
Extreme Environments ◽  
Abiotic Conditions ◽  
Culture Independent ◽  
Sequencing Platforms ◽  
Generation Sequencing ◽  
Culture Dependent

The deep sea (>1000 m below sea level) represents one of the most extreme environments of the ocean. Despite exhibiting harsh abiotic conditions such as low temperatures, high hydrostatic pressure, high salinity concentrations, a low input of organic matter, and absence of light, the deep sea encompasses a great fungal diversity. For decades, most knowledge on the fungal diversity of the deep sea was obtained through culture-dependent techniques. More recently, with the latest advances of high-throughput next generation sequencing platforms, there has been a rapid increment in the number of studies using culture-independent techniques. This review brings into the spotlight the progress of the techniques used to assess the diversity and ecological role of the deep-sea mycobiota and provides an overview on how the omics technologies have contributed to gaining knowledge about fungi and their activity in poorly explored marine environments. Finally, current challenges and suggested coordinated efforts to overcome them are discussed.

Role of phyllosphere fungi of forest trees in the development of decomposer fungal communities and decomposition processes of leaf litter

2006 ◽  
Vol 52 (8) ◽  
pp. 701-716 ◽  
Author(s):  
T Osono
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Leaf Litter ◽  
Nutrient Dynamics ◽  
Fungal Communities ◽  
Forest Trees ◽  
Structural Components ◽  
Decomposition Processes ◽  
Phyllosphere Fungi

The ecology of endophytic and epiphytic phyllosphere fungi of forest trees is reviewed with special emphasis on the development of decomposer fungal communities and decomposition processes of leaf litter. A total of 41 genera of phyllosphere fungi have been reported to occur on leaf litter of tree species in 19 genera. The relative proportion of phyllosphere fungi in decomposer fungal communities ranges from 2% to 100%. Phyllosphere fungi generally disappear in the early stages of decomposition, although a few species persist until the late stages. Phyllosphere fungi have the ability to utilize various organic compounds as carbon sources, and the marked decomposing ability is associated with ligninolytic activity. The role of phyllosphere fungi in the decomposition of soluble components during the early stages is relatively small in spite of their frequent occurrence. Recently, the roles of phyllosphere fungi in the decomposition of structural components have been documented with reference to lignin and cellulose decomposition, nutrient dynamics, and accumulation and decomposition of soil organic matter. It is clear from this review that several of the common phyllosphere fungi of forest trees are primarily saprobic, being specifically adapted to colonize and utilize dead host tissue, and that some phyllosphere fungi with marked abilities to decompose litter components play important roles in decomposition of structural components, nutrient dynamics, and soil organic matter accumulation.Key words: carbon cycle, community, endophyte, epiphyte, succession.

Arbuscular mycorrhizal fungal succession in a long-lived perennial

Botany ◽  
2014 ◽  
Vol 92 (4) ◽  
pp. 313-320 ◽  
Author(s):  
Miranda M. Hart ◽  
Monika Gorzelak ◽  
Diane Ragone ◽  
Susan J. Murch
Keyword(s):  
High Throughput Sequencing ◽  
Selective Pressure ◽  
Arbuscular Mycorrhizal ◽  
Am Fungi ◽  
Fungal Communities ◽  
Artocarpus Altilis ◽  
Host Identity ◽  
Arbuscular Mycorrhizal Fungal ◽  
Insight Into

It is difficult to understand why arbuscular mycorrhizal (AM) fungal communities change over time. The role of host identity confounds our understanding of successional changes in AM fungal communities because hosts exert strong selective pressure on their root-associated microbes. In this study we looked at the AM fungi associated with a long-lived perennial breadfruit (Artocarpus altilis (Parkinson) Fosberg) to see how AM communities change over the life span of a single, long-lived host. Using 454 high-throughput sequencing, we found evidence that older trees had more AM fungal taxa than younger trees and were associated with different AM fungal communities, but these differences were not apparent early in the life cycle. Older trees were dominated by species of Rhizophagus, whereas younger trees and genets were dominated by species of Glomus. Some taxa were only detected in older trees (e.g., Funneliformis) or genets (e.g., Racocetra and Scutellospora), indicating that certain AM fungal taxa may serve as “indicators” of the successional age of the fungal community. These results provide important information about a poorly studied system and give insight into how AM communities change over longer time scales.

scholarly journals Micro-aggregation of a pristine grassland soil selects for bacterial and fungal communities and changes in nitrogen cycling potentials

2021 ◽  
Author(s):  
Christoph Keuschnig ◽  
Jean Martins ◽  
Aline Navel ◽  
Pascal Simonet ◽  
Catherine Larose
Keyword(s):  
Particle Size ◽  
Nitrogen Cycling ◽  
Bacterial Communities ◽  
Soil Microbial Communities ◽  
Microbial Interactions ◽  
Fungal Communities ◽  
Supernatant Fraction ◽  
Soil Microbial ◽  
Microbial Analysis

Microbial analysis at the micro scale of soil is essential to the overall understanding of microbial organization and interactions, and necessary for a better understanding of soil ecosystem functioning. While bacterial communities have been extensively described, little is known about the organization of fungal communities as well as functional potentials at scales relevant to microbial interactions. Fungal and bacterial communities and changes in nitrogen cycling potentials in the pristine Rothamsted Park Grass soil (bulk soil) as well as in its particle size sub-fractions (PSFs; > 250 µm, 250-63 µm, 63-20 µm, 20-2 µm, < 2 µm and supernatant) were studied. The potential for nitrogen reduction was found elevated in bigger aggregates. The relative abundance of Basidiomycota deceased with decreasing particle size, Ascomycota showed an increase and Mucoromycota became more prominent in particles less than 20 µm. Bacterial community structures changed below 20 µm at the scale where microbes operate.Strikingly, only members of two bacterial and one fungal phyla (Proteobacteria, Bacteroidota and Ascomycota, respectively) were washed-off the soil during fractionation and accumulated in the supernatant fraction where most of the detected bacterial genera (e.g., Pseudomonas, Massilia, Mucilaginibacter, Edaphobaculum, Duganella, Janthinobacterium and Variovorax) were previously associated with exopolysaccharide production and biofilm formation.Overall, the applied method shows potential to study soil microbial communities at micro scales which might be useful in studies focusing on the role of specific fungal taxa in soil structure formation as well as research on how and by whom biofilm-like structures are distributed and organized in soil.

scholarly journals Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Pengfan Zhang ◽  
Stjin Spaepen ◽  
Yang Bai ◽  
Stephane Hacquard ◽  
Ruben Garrido-Oter
Keyword(s):  
Microbial Communities ◽  
Amplicon Sequencing ◽  
Fungal Communities ◽  
Polymorphic Variation ◽  
Sequencing Data ◽  
Sequencing Errors ◽  
Extensive Evaluation ◽  
Culture Independent ◽  
Reference Sequences ◽  
Synthetic Microbial Communities

AbstractSynthetic microbial communities (SynComs) constitute an emerging and powerful tool in biological, biomedical, and biotechnological research. Despite recent advances in algorithms for the analysis of culture-independent amplicon sequencing data from microbial communities, there is a lack of tools specifically designed for analyzing SynCom data, where reference sequences for each strain are available. Here we present Rbec, a tool designed for the analysis of SynCom data that accurately corrects PCR and sequencing errors in amplicon sequences and identifies intra-strain polymorphic variation. Extensive evaluation using mock bacterial and fungal communities show that our tool outperforms current methods for samples of varying complexity, diversity, and sequencing depth. Furthermore, Rbec also allows accurate detection of contaminants in SynCom experiments.

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