Unlocking the Microbiome Communities of Banana (Musa spp.) under Disease Stressed (Fusarium wilt) and Non-Stressed Conditions

Abstract Background: Plant harbours microbial communities in rhizosphere and inside the roots. These plants associated microbial communities play pivotal roles in plant growth and productivity. However, in banana, the microbiome assembly, composition and abundance in different plant organs is not well understood and restricted only to bacterial communities in rhizosphere. Results: We assessed the diversity, structure and assemblage of bacterial and fungal communities associated with banana plants with and without Fusarium oxysporum f. sp. cubense (Foc) symptoms. A total of 117,814 bacterial and 17,317 fungal operational taxonomy units (OTUs) were identified in the rhizosphere, roots and corm of the host plant. Results revealed that bacterial and fungal microbiota present in roots and corm primarily emanated from the rhizosphere. The composition of bacterial communities in the rhizosphere, roots and corm were different, with more diversity observed in the rhizosphere and less in the corm. However, distinct sample types i.e. without (asymptomatic) and with (symptomatic) Fusarium symptoms were the major drivers of the fungal community composition. Considering the high relative abundance among samples, we identified core microbiomes with bacterial and fungal OTUs classified into 20 families and colonizing distinct plant components of banana. Our core microbiome assigned 129 bacterial and 37 fungal genera to known taxa. Conclusions: Banana plants harbor a rich and diverse bacterial and fungal communities in the rhizosphere, roots and corm. By comparing communities in other crops, we state that several of the communities discovered in banana could serve as key nodes for plant growth and health.

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The gut mycobiome of healthy mice is shaped by the environment and shapes metabolic outcomes in response to diet

10.1101/2020.06.25.158287 ◽

2020 ◽

Author(s):

Tahliyah S. Mims ◽

Qusai Al Abdullah ◽

Justin D. Stewart ◽

Sydney P. Watts ◽

Catrina T. White ◽

...

Keyword(s):

Community Composition ◽

Fungal Community ◽

Bacterial Communities ◽

Genetic Background ◽

Dietary Exposure ◽

Fungal Communities ◽

Metabolic Adaptation ◽

Fungal Community Composition ◽

Metabolic Outcomes ◽

Metabolic Biomarkers

ABSTRACTObjectiveAs an active interface between the host and their diet, the gut bacteriome influences host metabolic adaptation. However, the contribution of gut fungi to host metabolic outcomes is not yet understood. Therefore, we aimed to determine if host metabolic response to an ultra-processed diet reflects gut fungal community composition.DesignWe compared jejunal fungi and bacteria from 72 healthy mice with the same genetic background but different starting mycobiomes before and after 8 weeks on an ultra-processed or standardized diet using 16S and internal transcribed spacer region 2 ribosomal RNA sequencing. We measured host body composition using magnetic resonance imaging, examined changes in metabolically active host tissues and quantified serum metabolic biomarkers.ResultsGut fungal communities are highly variable between mice, differing by vendor, age and sex. After exposure to an ultra-processed diet for 8 weeks, persistent differences in fungal community composition strongly associate with differential deposition of body mass in male mice compared to mice on standardized diet. Fat deposition in the liver, genomic adaptation of metabolically active tissues and serum metabolic biomarkers are correlated with alterations in fungal diversity and community composition. Variation in fungi from the genera Thermomyces and Saccharomyces most strongly associate with increased weight gain.ConclusionsIn the gut of healthy mice, host-microbe metabolic interactions strongly reflect variability in fungal communities. Our results confirm the importance of luminal fungal communities to host metabolic adaptation to dietary exposure. Gut fungal communities may represent a therapeutic target for the prevention and treatment of metabolic disease.Graphical AbstractIn BriefWhat is already known about this subject?Gut bacterial communities have evolved to influence the metabolic outcomes of the host in mammals. Evidence from across the lifespan suggests that differences in composition of these communities is associated with energy consumption. However, gut microbial communities, while often equated to bacteria, are diverse, multi-kingdom ecologies and limited information is available for the role of other kingdoms of life, such as fungi.What are the new findings?Gut fungal communities, collectively termed the mycobiome, are less diverse and abundant than bacterial communities in the gastrointestinal tract. This study identifies the considerable influence of the environment and dietary exposure on the composition of jejunal fungal communities in healthy mice with the same genetic background. After exposure to processed diet, differences in fungal community composition in male mice were strongly correlated with persistent differences body composition and markers of metabolic tone.How might it impact on clinical practice in the foreseeable future?These results verify that the baseline metabolic tone of health mice strongly reflects the ecological complexity of the gastrointestinal mycobiome. Variation in the composition of gut fungal communities is likely an underappreciated source of experimental and clinical variability in metabolic studies. Gastrointestinal fungi are likely a target for prevention and treatment of metabolic disease.

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Mycobiome Composition and Diversity under the Long-Term Application of Spent Mushroom Substrate and Chicken Manure

Agronomy ◽

10.3390/agronomy11030410 ◽

2021 ◽

Vol 11 (3) ◽

pp. 410

Author(s):

Magdalena Frąc ◽

Giorgia Pertile ◽

Jacek Panek ◽

Agata Gryta ◽

Karolina Oszust ◽

...

Keyword(s):

Relative Abundance ◽

Fungal Community ◽

Denaturing Gradient Gel Electrophoresis ◽

Crop Protection ◽

Cropping System ◽

Chicken Manure ◽

Spent Mushroom Substrate ◽

Organic Additives ◽

Fungal Community Composition ◽

Chain Reactions

Waste exogenous organic matter, including spent mushroom substrate (SMS) and chicken manure (CM), can be used as the basis of a soil-improving cropping system in sustainable agriculture. However, there is—as yet—a lack of information about important quality indicators such as the fungal community relative abundance, structure and biodiversity in soils treated with these additives. In this study, the responses of the soil fungal community composition and mycobiome diversity to SMS and CM application compared to the control soil were evaluated using a combination of the following molecular approaches: quantitative polymerase chain reactions, denaturing gradient gel electrophoresis, terminal restriction fragment length polymorphism, and next-generation sequencing. The most abundant phylum for both treatments was Ascomycota, followed by Basidiomycota. The application of SMS and CM increased the abundance of fungi, including Tremellomycetes and Pezizomycetes for the SMS additive, while the Mortierellomycetes, Pezizomycetes, and Leotiomycetes levels increased after CM addition. SMS and CM beneficially reduced the relative abundance of several operational taxonomic units (OTUs) which are potential crop pathogens. The results provide a novel insight into the fungal community associated with organic additives, which should be beneficial in the task of managing the soil mycobiome as well as crop protection and productivity.

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Ecological networks reveal contrasting patterns of bacterial and fungal communities in glacier-fed streams in Central Asia

10.7287/peerj.preprints.27887 ◽

2019 ◽

Cited By ~ 1

Author(s):

Ze Ren ◽

Hongkai Gao

Keyword(s):

Bacterial Community ◽

Microbial Communities ◽

Central Asia ◽

Fungal Community ◽

Bacterial Communities ◽

Beta Diversity ◽

Hydrological Modeling ◽

Alpha Diversity ◽

Environmental Variation ◽

Fungal Communities

Bacterial and fungal communities in biofilms are important components in driving biogeochemical processes in stream ecosystems. Previous studies have well documented the patterns of bacterial alpha diversity in stream biofilms in glacier-fed streams, where, however, beta diversity of the microbial communities has received much less attention especially considering both bacterial and fungal communities. A focus on beta diversity can provide insights into the mechanisms driving community changes associated to large environmental fluctuations and disturbances, such as in glacier-fed streams. Moreover, modularity of co-occurrence networks can reveal more ecological and evolutionary properties of microbial communities beyond taxonomic groups. Here, integrating beta diversity and co-occurrence approach, we explored the network topology and modularity of the bacterial and fungal communities with consideration of environmental variation in glacier-fed streams in Central Asia. Combining results from hydrological modeling and normalized difference of vegetation index, this study highlighted that hydrological variables and vegetation status are major variables determining the environmental heterogeneity of glacier-fed streams. Bacterial communities formed a more complex and connected network, while the fungal communities formed a more clustered network. Moreover, the strong interrelations among the taxonomic dissimilarities of bacterial community and modules suggest they had common processes in driving diversity and taxonomic compositions across the heterogeneous environment. In contrast, fungal community and modules generally showed distinct driving processes to each other. Moreover, bacterial and fungal communities also had different driving processes. Furthermore, the variation of bacterial community and modules were strongly correlated with hydrological properties and vegetation status but not with nutrients, while fungal community and modules (except one module) were not associated with environmental variation. Our results suggest that bacterial and fungal communities had distinct mechanisms in structuring microbial networks, and environmental variation had strong influences on bacterial communities but not on fungal communities. The fungal communities have unique assembly mechanisms and physiological properties which might lead to their insensitive responses to environmental variations compared to bacterial communities. Overall, beyond alpha diversity in previous studies, these results add our knowledge that bacterial and fungal communities have contrasting assembly mechanisms and respond differently to environmental variation in glacier-fed streams.

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Ecological networks reveal contrasting patterns of bacterial and fungal communities in glacier-fed streams in Central Asia

10.7287/peerj.preprints.27887v1 ◽

2019 ◽

Author(s):

Ze Ren ◽

Hongkai Gao

Keyword(s):

Bacterial Community ◽

Microbial Communities ◽

Central Asia ◽

Fungal Community ◽

Bacterial Communities ◽

Beta Diversity ◽

Hydrological Modeling ◽

Alpha Diversity ◽

Environmental Variation ◽

Fungal Communities

Bacterial and fungal communities in biofilms are important components in driving biogeochemical processes in stream ecosystems. Previous studies have well documented the patterns of bacterial alpha diversity in stream biofilms in glacier-fed streams, where, however, beta diversity of the microbial communities has received much less attention especially considering both bacterial and fungal communities. A focus on beta diversity can provide insights into the mechanisms driving community changes associated to large environmental fluctuations and disturbances, such as in glacier-fed streams. Moreover, modularity of co-occurrence networks can reveal more ecological and evolutionary properties of microbial communities beyond taxonomic groups. Here, integrating beta diversity and co-occurrence approach, we explored the network topology and modularity of the bacterial and fungal communities with consideration of environmental variation in glacier-fed streams in Central Asia. Combining results from hydrological modeling and normalized difference of vegetation index, this study highlighted that hydrological variables and vegetation status are major variables determining the environmental heterogeneity of glacier-fed streams. Bacterial communities formed a more complex and connected network, while the fungal communities formed a more clustered network. Moreover, the strong interrelations among the taxonomic dissimilarities of bacterial community and modules suggest they had common processes in driving diversity and taxonomic compositions across the heterogeneous environment. In contrast, fungal community and modules generally showed distinct driving processes to each other. Moreover, bacterial and fungal communities also had different driving processes. Furthermore, the variation of bacterial community and modules were strongly correlated with hydrological properties and vegetation status but not with nutrients, while fungal community and modules (except one module) were not associated with environmental variation. Our results suggest that bacterial and fungal communities had distinct mechanisms in structuring microbial networks, and environmental variation had strong influences on bacterial communities but not on fungal communities. The fungal communities have unique assembly mechanisms and physiological properties which might lead to their insensitive responses to environmental variations compared to bacterial communities. Overall, beyond alpha diversity in previous studies, these results add our knowledge that bacterial and fungal communities have contrasting assembly mechanisms and respond differently to environmental variation in glacier-fed streams.

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Diversity and Structure of Soil Fungal Communities across Experimental Everglades Tree Islands

Diversity ◽

10.3390/d12090324 ◽

2020 ◽

Vol 12 (9) ◽

pp. 324

Author(s):

Brianna K. Almeida ◽

Michael S. Ross ◽

Susana L. Stoffella ◽

Jay P. Sah ◽

Eric Cline ◽

...

Keyword(s):

Water Level ◽

Fungal Community ◽

Plant Pathogen ◽

Fungal Diversity ◽

Fungal Communities ◽

Tree Islands ◽

Fungal Community Composition ◽

Everglades Tree Islands ◽

And Function ◽

Early Restoration

Fungi play prominent roles in ecosystem services (e.g., nutrient cycling, decomposition) and thus have increasingly garnered attention in restoration ecology. However, it is unclear how most management decisions impact fungal communities, making it difficult to protect fungal diversity and utilize fungi to improve restoration success. To understand the effects of restoration decisions and environmental variation on fungal communities, we sequenced soil fungal microbiomes from 96 sites across eight experimental Everglades tree islands approximately 15 years after restoration occurred. We found that early restoration decisions can have enduring consequences for fungal communities. Factors experimentally manipulated in 2003–2007 (e.g., type of island core) had significant legacy effects on fungal community composition. Our results also emphasized the role of water regime in fungal diversity, composition, and function. As the relative water level decreased, so did fungal diversity, with an approximately 25% decline in the driest sites. Further, as the water level decreased, the abundance of the plant pathogen–saprotroph guild increased, suggesting that low water may increase plant-pathogen interactions. Our results indicate that early restoration decisions can have long-term consequences for fungal community composition and function and suggest that a drier future in the Everglades could reduce fungal diversity on imperiled tree islands.

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Crop, genotype, and field environmental conditions shape bacterial and fungal seed epiphytic microbiomes

Canadian Journal of Microbiology ◽

10.1139/cjm-2020-0306 ◽

2020 ◽

pp. 1-13

Author(s):

Zayda P. Morales Moreira ◽

Bobbi L. Helgason ◽

James J. Germida

Keyword(s):

Environmental Conditions ◽

Amplicon Sequencing ◽

Fungal Communities ◽

Plant Fitness ◽

Microbial Composition ◽

Core Microbiome ◽

Reproductive Structures ◽

Microbial Assemblage ◽

Crop Type ◽

Diversity Structure

Seeds are reproductive structures able to carry and transfer microorganisms that play an important role in plant fitness. Genetic and external factors are reported to be partly responsible for the plant microbiome assemblage, but their contribution in seeds is poorly understood. In this study, wheat, canola, and lentil seeds were analyzed to characterize diversity, structure, and persistence of seed-associated microbial communities. Five lines and 2 generations of each crop were subjected to high-throughput amplicon sequencing of the 16S rRNA and internal transcribed spacer (ITS) regions. Bacterial and fungal communities differed most by crop type (30% and 47% of the variance), while generation explained an additional 10% and 15% of the variance. The offspring (i.e., generation harvested in 2016 at the same location) exhibited a higher number of common amplicon sequence variants (ASVs) and less variability in microbial composition. Additionally, in every sample analyzed, a “core microbiome” was detected consisting of 5 bacterial and 12 fungal ASVs. Our results suggest that crop, genotype, and field environmental conditions contributed to the seed-associated microbial assemblage. These findings not only expand our understanding of the factors influencing the seed microbiome but may also help us to manipulate and exploit the microbiota naturally carried by seeds.

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Long-Term Monoculture Negatively Regulates Fungal Community Composition and Abundance of Tea Orchards

Agronomy ◽

10.3390/agronomy9080466 ◽

2019 ◽

Vol 9 (8) ◽

pp. 466 ◽

Cited By ~ 4

Author(s):

Yasir Arafat ◽

Muhammad Tayyab ◽

Muhammad Umar Khan ◽

Ting Chen ◽

Hira Amjad ◽

...

Keyword(s):

Soil Ph ◽

Fungal Community ◽

Cropping System ◽

Alpha Diversity ◽

Fungal Species ◽

Fungal Communities ◽

Continuous Cropping ◽

Fungal Community Composition ◽

Continuous Cropping System ◽

Tea Plants

Continuous cropping frequently leads to soil acidification and major soil-borne diseases in tea plants, resulting in low tea yield. We have limited knowledge about the effects of continuous tea monoculture on soil properties and the fungal community. Here, we selected three replanted tea fields with 2, 15, and 30 years of monoculture history to assess the influence of continuous cropping on fungal communities and soil physiochemical attributes. The results showed that continuous tea monoculture significantly reduced soil pH and tea yield. Alpha diversity analysis showed that species richness declined significantly as the tea planting years increased and the results based on diversity indicated inconsistency. Principal coordinate analysis (PCoA) revealed that monoculture duration had the highest loading in structuring fungal communities. The relative abundance of Ascomycota, Glomeromycota, and Chytridiomycota decreased and Zygomycota and Basidiomycota increased with increasing cropping time. Continuous tea cropping not only decreased some beneficial fungal species such as Mortierella alpina and Mortierella elongatula, but also promoted potentially pathogenic fungal species such as Fusarium oxysporum, Fusarium solani, and Microidium phyllanthi over time. Overall, continuous tea cropping decreased soil pH and potentially beneficial microbes and increased soil pathogenic microbes, which could be the reason for reducing tea yield. Thus, developing sustainable tea farming to improve soil pH, microbial activity, and enhanced beneficial soil microbes under a continuous cropping system is vital for tea production.

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Fast response of fungal and prokaryotic communities to climate change manipulation in two contrasting tundra soils

Environmental Microbiome ◽

10.1186/s40793-019-0344-4 ◽

2019 ◽

Vol 14 (1) ◽

Author(s):

Jana Voříšková ◽

Bo Elberling ◽

Anders Priemé

Keyword(s):

Organic Matter ◽

Seasonal Variation ◽

Snow Cover ◽

Bacterial Communities ◽

Winter Precipitation ◽

Fungal Communities ◽

Tundra Soils ◽

Short Term ◽

Fungal Community Composition ◽

Climate Manipulation

Abstract Background Climate models predict substantial changes in temperature and precipitation patterns across Arctic regions, including increased winter precipitation as snow in the near future. Soil microorganisms are considered key players in organic matter decomposition and regulation of biogeochemical cycles. However, current knowledge regarding their response to future climate changes is limited. Here, we explore the short-term effect of increased snow cover on soil fungal, bacterial and archaeal communities in two tundra sites with contrasting water regimes in Greenland. In order to assess seasonal variation of microbial communities, we collected soil samples four times during the plant-growing season. Results The analysis revealed that soil microbial communities from two tundra sites differed from each other due to contrasting soil chemical properties. Fungal communities showed higher richness at the dry site whereas richness of prokaryotes was higher at the wet tundra site. We demonstrated that fungal and bacterial communities at both sites were significantly affected by short-term increased snow cover manipulation. Our results showed that fungal community composition was more affected by deeper snow cover compared to prokaryotes. The fungal communities showed changes in both taxonomic and ecological groups in response to climate manipulation. However, the changes were not pronounced at all sampling times which points to the need of multiple sampling in ecosystems where environmental factors show seasonal variation. Further, we showed that effects of increased snow cover were manifested after snow had melted. Conclusions We demonstrated rapid response of soil fungal and bacterial communities to short-term climate manipulation simulating increased winter precipitation at two tundra sites. In particular, we provide evidence that fungal community composition was more affected by increased snow cover compared to prokaryotes indicating fast adaptability to changing environmental conditions. Since fungi are considered the main decomposers of complex organic matter in terrestrial ecosystems, the stronger response of fungal communities may have implications for organic matter turnover in tundra soils under future climate.

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Limited Effects of Variable-Retention Harvesting on Fungal Communities Decomposing Fine Roots in Coastal Temperate Rainforests

Applied and Environmental Microbiology ◽

10.1128/aem.02061-17 ◽

2017 ◽

Vol 84 (3) ◽

Cited By ~ 2

Author(s):

Timothy J. Philpott ◽

Jason S. Barker ◽

Cindy E. Prescott ◽

Sue J. Grayston

Keyword(s):

Community Composition ◽

Fungal Community ◽

Fine Roots ◽

Fine Root ◽

Plant Litter ◽

Fungal Communities ◽

Decomposition Rates ◽

Fungal Community Composition ◽

Variable Retention ◽

Variable Retention Harvesting

ABSTRACT Fine root litter is the principal source of carbon stored in forest soils and a dominant source of carbon for fungal decomposers. Differences in decomposer capacity between fungal species may be important determinants of fine-root decomposition rates. Variable-retention harvesting (VRH) provides refuge for ectomycorrhizal fungi, but its influence on fine-root decomposers is unknown, as are the effects of functional shifts in these fungal communities on carbon cycling. We compared fungal communities decomposing fine roots (in litter bags) under VRH, clear-cut, and uncut stands at two sites (6 and 13 years postharvest) and two decay stages (43 days and 1 year after burial) in Douglas fir forests in coastal British Columbia, Canada. Fungal species and guilds were identified from decomposed fine roots using high-throughput sequencing. Variable retention had short-term effects on β-diversity; harvest treatment modified the fungal community composition at the 6-year-postharvest site, but not at the 13-year-postharvest site. Ericoid and ectomycorrhizal guilds were not more abundant under VRH, but stand age significantly structured species composition. Guild composition varied by decay stage, with ruderal species later replaced by saprotrophs and ectomycorrhizae. Ectomycorrhizal abundance on decomposing fine roots may partially explain why fine roots typically decompose more slowly than surface litter. Our results indicate that stand age structures fine-root decomposers but that decay stage is more important in structuring the fungal community than shifts caused by harvesting. The rapid postharvest recovery of fungal communities decomposing fine roots suggests resiliency within this community, at least in these young regenerating stands in coastal British Columbia. IMPORTANCE Globally, fine roots are a dominant source of carbon in forest soils, yet the fungi that decompose this material and that drive the sequestration or respiration of this carbon remain largely uncharacterized. Fungi vary in their capacity to decompose plant litter, suggesting that fungal community composition is an important determinant of decomposition rates. Variable-retention harvesting is a forestry practice that modifies fungal communities by providing refuge for ectomycorrhizal fungi. We evaluated the effects of variable retention and clear-cut harvesting on fungal communities decomposing fine roots at two sites (6 and 13 years postharvest), at two decay stages (43 days and 1 year), and in uncut stands in temperate rainforests. Harvesting impacts on fungal community composition were detected only after 6 years after harvest. We suggest that fungal community composition may be an important factor that reduces fine-root decomposition rates relative to those of above-ground plant litter, which has important consequences for forest carbon cycling.

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