Lower Fungal Diversity Research Articles

Management of industrial wine residues: physicochemical, bacterial and fungal dynamics during composting processes

To foster a circular bioeconomy throughout the management of industrial solid wine residues in the wine industry, this work presents the physicochemical and microbiological dynamics of the composting process with white grape pomace, stalks and wastewater treatment plant sludge from the same winery. Three composting windrows of 41 m3 were constructed with 0, 10 and 20% sludge addition. Physicochemical parameters were assessed following the Test Method for the Examination of Composting and Compost (TMECC), and the diversity and dynamics of the bacterial and fungal communities involved in the composting process were assessed via a high-throughput sequencing metabarcoding approach. The addition of sludge increased the moisture content, bulk density, and pH after six months of turned windrow composting. No effect of sludge addition on the macronutrient composition of the compost was observed. The Shannon‒Wiener index differed among stages and treatments. Bacterial diversity increased over time, while the fungal community appeared to be highly affected by the thermophilic stage, which led to a reduction in diversity that slightly recovered by the end of the process. Furthermore, the sludge exhibited high bacterial diversity but very low fungal diversity. Consequently, the design of on-site biologically based strategies to better manage wine residues can produce soil amendments, improve fertilization, reclaim damaged soils, and ultimately reduce management costs, making composting an economically attractive and sustainable alternative for waste management in the wine industry.Graphical

Checklist of Macrofungi Associated with Nine Different Habitats of Taburno-Camposauro Massif in Campania, Southern Italy.

The checklist serves as an informative method for evaluating the diversity, geography, and ecology of established and reproducing macrofungi. Additionally, considering macrofungi as bioindicator species, their census should be incorporated into efforts to monitor the state of health of ecosystems and directly applied to conservation policies. Between 2019 and 2023, a census of macrofungal species was conducted in Taburno-Camposauro Regional Park (Campania, Italy) across nine distinct habitats. A total of 453 fungal taxa were identified, including several new records for the Campania region. The fungal diversity exhibited significant variations based on the dominant plant species in each habitat. Fagacean tree species and Carpinus spp. shared similar fungal communities. Equally, coniferous tree species displayed a comparable fungal composition. In Abies alba and mixed broad-leaved forests, low levels of ectomycorrhizal taxa were observed alongside a concurrent increase in saprotrophs, indicating a disturbed habitat and a reduction in the Gadgil effect. Notably, lower fungal diversity was documented in the grassland habitat, suggesting the potential implications of wildlife imbalance and excessive grazing. The provided checklist constitutes a valuable resource for local management authorities, providing insights to formulate specific management policies.

Wide divergence of fungal communities inhabiting rocks and soils in a hyper-arid Antarctic desert.

Highly simplified microbial communities colonise rocks and soils of continental Antarctica ice-free deserts. These two habitats impose different selection pressures on organisms, yet the possible filtering effects on the diversity and composition of microbial communities have not hitherto been fully characterised. We hence compared fungal communities in rocks and soils in three localities of inner Victoria Land. We found low fungal diversity in both substrates, with a mean species richness of 28 across all samples, and significantly lower diversity in rocks than in soils. Rock and soil communities were strongly differentiated, with a multinomial species classification method identifying just three out of 328 taxa as generalists with no affinity for either substrate. Rocks were characterised by a higher abundance of lichen-forming fungi (typically Buellia, Carbonea, Pleopsidium, Lecanora, and Lecidea), possibly owing to the more protected environment and the porosity of rocks permitting photosynthetic activity. In contrast, soils were dominated by obligate yeasts (typically Naganishia and Meyerozyma), the abundances of which were correlated with edaphic factors, and the black yeast Cryomyces. Our study suggests that strong differences in selection pressures may account for the wide divergences of fungal communities in rocks and soils of inner Victoria Land.

Oral fungal profiling and risk of nasopharyngeal carcinoma: a population-based case-control study

Dysbiosis of the oral mycobiome has been linked to some diseases, including cancers. However, the role of oral fungal communities in nasopharyngeal carcinoma (NPC) carcinogenesis has not previously been investigated. We characterized the oral salivary fungal mycobiome in 476 untreated incident NPC patients and 537 population-based controls using fungal internal transcribed spacer (ITS)-2 sequencing. The relationship between oral fungal mycobiome and the risk of NPC was assessed through bioinformatic and biostatistical analyses. We found that lower fungal alpha diversity was associated with an increased odds of NPC [lower vs. higher: observed features (adjusted odds ratio [OR]=5.81, 95% confidence interval [CI]=3.60-9.38); Simpson diversity (1.53, 1.03-2.29); Shannon diversity (2.03, 1.35-3.04)]. We also observed a significant difference in global fungal community patterns between cases and controls based on Bray-Curtis dissimilarity (P<0.001). Carriage of oral fungal species, specifically, Saccharomyces cerevisiae, Candida tropicalis, Lodderomyces elongisporus, Candida albicans, and Fusarium poae, was associated with significantly higher odds of NPC, with ORs ranging from 1.56 to 4.66. Individuals with both low fungal and low bacterial alpha diversity had a profoundly elevated risk of NPC. Our results suggest that dysbiosis in the oral mycobiome, characterized by a loss of fungal community diversity and overgrowth of several fungal organisms, is associated with a substantially increased risk of NPC. This work was funded by the US National Institutes of Health, the Swedish Research Council, the High-level Talents Research Start-up Project of Fujian Medical University, and the China Scholarship Council.

How does land-use change alter soil microbial diversity, composition, and network in subtropical China?

Soil microbial communities play essential roles in degraded soil ecosystems. The “emergent trait” indices (e.g., microbial biomass C and N, and enzyme activity) and specific soil microbiota associations have been intensively studied, but the responses of soil microbial composition and network complexities to land-use changes remain unclear. Using amplicon sequencing of 16S rRNA genes and internal transcribed spacer (ITS) regions, we assessed the response ratio of soil microbial genomic diversity, community structure, and network parameters to primary evergreen broadleaved forest (control) conversion to conifer plantations, orchards, sloping tillage, and paddy fields. Agricultural lands had a higher soil bacterial and lower fungal diversity than primary forest. Overall, primary forest conversion reduced microbial network complexity, except in the sloping tillage. Moreover, land-use changes shifted the microbial community composition by either decreasing or increasing the relative abundance of dominant and putative keystone associations. The mean response ratio (indicator response percentage to primary forest conversion) of the microbial index to the land-use change varied depending on the soil microbial alpha diversity, network topological parameters, and dominant and putative keystone associations. Alterations in soil microbial diversity, composition, and network complexity were related to reduced soil resource availability following land-use change. Our study suggested that primary forest conversion to agricultural lands did not always negatively influences soil microbial diversity, composition, network complexity, and putative keystone associations. In addition, specific soil microbial associations showed highly sensitive to land-use change.

Short‐term effects of mineral and combined mineral‐organic fertilization in soil microbial communities

AbstractFertilization is a widely used practice to maintain soil fertility. To unravel the rapid response patterns of soil microbial under mineral and combined mineral‐organic fertilization treatments, 1‐year fertilization trial was conducted in an intensive greenhouse on the Qinghai‐Tibet Plateau (QTP). Higher soil nutrient concentrations and lower soil pH were detected in mineral and combined mineral‐organic fertilized soils than in unfertilized soils. Both fertilized soils also showed higher bacterial richness and diversity and lower fungal diversity than unfertilized soils. Compared with the soil without fertilizer application, the soil microflora structure was significantly changed by fertilizer application; however, no differences were detected between both fertilized soils. Both short‐term fertilizations recruited more abundant Proteobacteria and Ascomycota, and a smaller proportion of Acidobacteriota, Basidiomycota and Mortierellomycota. In addition, available phosphorus (AP), was most closely linked to the variations in the structures of soil bacterial and fungal communities. Our findings highlight the significance of the temporal component for fertilization effects, indicating that 1 year of mineral and combined mineral‐organic fertilization only affected the diversity of some bacterial and fungal communities in the soil. Therefore, a moderately longer fertilization year based on this study should be pondered in intensive greenhouse cultivation in the QTP.

Epiphitic Microbiome of Alvarinho Wine Grapes from Different Geographic Regions in Portugal

Geographic location and, particularly, soil and climate exert influence on the typicality of a wine from a specific region, which is often justified by the terroir, and these factors also influence the epiphytic flora associated with the surface of the grape berries. In the present study, the microbiome associated with the surface of berries obtained from ten vineyards of the Alvarinho variety located in different geographical locations in mainland Portugal was determined and analyzed. The removal of microbial flora from the surface of the berries was carried out by washing and sonication, after which the extraction and purification of the respective DNA was carried out. High-throughput short amplicon sequencing of the fungal ITS region and the bacterial 16S region was performed, allowing for the determination of the microbial consortium associated with Alvarinho wine grapes. Analysis of α-diversity demonstrated that parcels from the Monção and Melgaço sub-region present a significantly (p < 0.05) lower fungal diversity and species richness when compared to the plots analyzed from other regions/sub-regions. The ubiquitous presence of Metschnikowia spp., a yeast with enologic potential interest in all parcels from Monção and Melgaço, was also observed.

A Stronger Rhizosphere Impact on the Fungal Communities Compared to the Bacterial Communities in Pecan Plantations.

Understanding microbial communities associated with bulk and rhizosphere soils will benefit the maintenance of forest health and productivity and the sustainable development of forest ecosystems. Based on MiSeq sequencing, we explored the differences between the bulk soil and the rhizosphere soil on bacterial and fungal communities of pecan plantation. Results suggested that rhizosphere-associated fungal rather than bacterial community structures differed from bulk soil, and rhizosphere soil had lower fungal diversity than bulk soil. Actinobacteria and Cantharellales were the bacterial and fungal biomarkers of the rhizosphere soil of pecan plantation, respectively. In addition, Pleosporales, which are mainly involved in saprophylaxis and plant pathogenic processes, was identified as one of the most important fungal biomarkers for the bulk soil, and the FunGuild predicted a higher relative abundance of pathogenic fungi in bulk soil compared to rhizosphere soil. The pH, ammonium nitrogen (-N), nitrate nitrogen (-N), and total carbon (TC) contents drove microbial community structure and composition. The bacterial network was simpler in the rhizosphere soil than in the bulk soil. However, fungi showed the opposite network pattern. Keystone species in bacterial and fungal networks were mostly involved in nutrient cycling and the C cycling, and were found to be enriched in the rhizosphere soil. Overall, in terms of bacterial and fungal communities, the rhizosphere soil behaves more healthily than the bulk soil and has a higher potential for nutrient cycling.

Glacier Retreat Results in Loss of Fungal Diversity

Walker Glacier near the northern coast of Ellesmere Island in the Canadian High Arctic (terrestrial margin of the ‘Last Ice Area’) is undergoing rapid ice attrition in response to climate change. We applied culture and molecular methods to investigate fungal diversity at the terminus of this glacier. Analysis of the mycoflora composition showed that the Walker Glacier isolates separated into two clusters: the surface of the glacier ice and the glacier foreland. The recently exposed sediments of the foreland had a lower fungal diversity and different species from those on the ice, with the exception of five species that occurred in both habitats. This loss of glacial ice in the Arctic is therefore resulting in the loss of habitats for cold-dwelling fungal species. Fungal diversity is a potentially rich biological resource of glacial ecosystems, with unique taxa. The rapid loss of these glacial habitats underscores the urgency for genomic surveys of fungal diversity in the High Arctic, and the need for further isolation of strains as well as cryopreservation of environmental micro-biome samples for future research and conservation.

Diversity and structure of the rhizosphere microbial communities of wild and cultivated ginseng

Background The resources of wild ginseng have been reducing sharply, and it is mainly dependent on artificial cultivation in China, Korea and Japan. Based on cultivation modes, cultivated ginseng include understory wild ginseng (the seeds or seedlings of cultivated ginseng were planted under the theropencedrymion without human intervention) and farmland cultivated ginseng (grown in farmland with human intervention). Cultivated ginseng, can only be planted on the same plot of land consecutively for several years owing to soilborne diseases, which is mainly because of the variation in the soil microbial community. In contrast, wild ginseng can grow for hundreds of years. However, the knowledge of rhizosphere microbe communities of the wild ginseng is limited.ResultIn the present study, the microbial communities in rhizosphere soils of the three types of ginseng were analyzed by high-throughput sequencing of 16 S rRNA for bacteria and internal transcribed spacer (ITS) region for fungi. In total, 4,381 bacterial operational taxonomic units (OTUs) and 2,679 fungal OTUs were identified in rhizosphere soils of the three types of ginseng. Among them, the shared bacterial OTUs was more than fungal OTUs by the three types of ginseng, revealing fungal communities were to be more affected than bacterial communities. In addition, the composition of rhizosphere microbial communities and bacterial diversity were similar between understory wild ginseng and wild ginseng. However, higher bacterial diversity and lower fungal diversity were found in rhizosphere soils of wild ginseng compared with farmland cultivated ginseng. Furthermore, the relative abundance of Chloroflexi, Fusarium and Alternaria were higher in farmland cultivated ginseng compared to wild ginseng and understory wild ginseng.ConclusionsOur results showed that composition and diversity of rhizosphere microbial communities were significantly different in three types of ginseng. This study extended the knowledge pedigree of the microbial diversity populating rhizospheres, and provided insights into resolving the limiting bottleneck on the sustainable development of P. ginseng crops, and even the other crops of Panax.

Fungal Interactions Matter: Tricholoma matsutake Domination Affect Fungal Diversity and Function in Mountain Forest Soils.

Simple SummaryTricholoma matsutake forms a symbiotic association with hosts, developing mycelial aggregations, called ‘shiro’. The fungal diversity living in shiro soil play key roles in nutrient cycles for this economically important mushroom, but have not been profiled across large spatial and environmental gradients. Here, we mainly aimed to study the fungal characteristics in the bulk soil (non-shiro) and shiro, using phospholipid fatty acids and illuninan sequencing in five habitats across landscapes in southwestern China. T. matsutake causes a lower fungal diversity and simplifies the fungal community composition in shiro soil compared with non-shiro soil across five forest types. We also found that geo-graphical proximity was accompanied by a similar fungal community structure but different contributions from specific species under five forest types. Among the co-existed fungi, Oidiodendron were found to collaborate with T. matsutake, whereas Helotiales and Mortierella showed a negative correlation with it. The selection of these taxa may be related to their ability to compete with resources and different nutrient strategists in the soil. Overall, we conclude that T. matsutake generate a dominance effect to shape the fungal community and diversity in shiro soil across distinctive forest types.Tricholoma matsutake forms a symbiotic association with coniferous trees, developing mycelial aggregations, called ‘shiro’, which are characterized by distinct chemical and physical properties from nearby forest bulk soil. The fungal diversity living in shiro soil play key roles in nutrient cycles for this economically important mushroom, but have not been profiled across large spatial and environmental gradients. Samples of shiro and non-shiro (nearby bulk soil) were taken from five field sites where sporocarps naturally formed. Phospholipid fatty acids (PLFA) and Illumina MiSeq sequencing were combined to identify fungal biomass and community structure. Matsutake dominated in the shiro, which had a significantly reduced saprotrophic fungi biomass compared to non-shiro soil. Fungal diversity was negatively correlated with the relative abundance of T. matsutake in the shiro soil. The fungal community in the shiro was characterized by similar fungal species composition in most samples regardless of forest types. Matsutake coexisted with a specific fungal community due to competition or nutrient interactions. Oidiodendron was positively correlated with the abundance of T. matsutake, commonly cohabitant in the shiro. In contrast, Helotiales and Mortierella were negatively correlated with T. matsutake, both of which commonly inhabit the non-shiro soil but do not occur in shiro soils. We conclude that T. matsutake generate a dominance effect to shape the fungal community and diversity in shiro soil across distinctive forest types.

Impact of Olive Saplings and Organic Amendments on Soil Microbial Communities and Effects of Mineral Fertilization.

Plant communities and fertilization may have an impact on soil microbiome. Most commercial olive trees are minerally fertilized, while this practice is being replaced by the use of organic amendments. Organic amendments can both fertilize and promote plant growth-promoting organisms. Our aims were (i) to describe the changes in soil bacterial and fungal communities induced by the presence of young olive trees and their interaction with organic amendments and (ii) to compare the effects of mineral and organic fertilization. We set up two parallel experiments in pots using a previously homogenized soil collected from a commercial olive orchard: in the first one, we grew olive saplings in unamended and organically amended soils with two distinct composts and compared these two soils incubated without a plant, while in the second experiment, we comparatively tested the effects of organic and mineral fertilization. OTUs and the relative abundances of bacterial and fungal genera and phyla were analyzed by 16S rRNA and ITS1 gene amplicon using high-throughput sequencing. Basal respiration and substrate-induced respiration were measured by MicroRespTM. The effects of the different treatments were analyzed in all phyla and in the 100 most abundant genera. The presence of olive saplings increased substrate-induced respiration and bacterial and fungal richness and diversity. Organic amendments greatly affected both bacterial and fungal phyla and increased bacterial richness while not affecting fungal richness. Mineral fertilization increased the relative abundance of the less metabolically active bacterial phyla (Actinobacteria and Firmicutes), while it reduced the most metabolically active phylum, Bacteroidetes. Mineral fertilization increased the relative abundance of three N2-fixing Actinobacteria genera, while organic fertilization only increased one genus of Proteobacteria. In organically and minerally fertilized soils, high basal respiration rates were associated with low fungal diversity. Basidiomycota and Chytridiomycota relative abundances positively correlated with basal respiration and substrate-induced respiration, while Ascomycota correlated negatively. Indeed, the Ascomycota phyla comprised most of the fungal genera decreased by organic amendments. The symbiotrophic phylum Glomeromycota did not correlate with any of the C sources. The relative abundance of this phylum was promoted by the presence of plants but decreased when amending soils with composts.

Parasites, niche modification and the host microbiome: A field survey of multiple parasites.

Parasites can affect and be affected by the host's microbiome, with consequences for host susceptibility, parasite transmission, and host and parasite fitness. Yet, two aspects of the relationship between parasite infection and host microbiota remain little understood: the nature of the relationship under field conditions, and how the relationship varies among parasites. To overcome these limitations, we performed a field survey of the within-leaf fungal community in a tall fescue population. We investigated how diversity and composition of the fungal microbiome associate with natural infection by fungal parasites with different feeding strategies. A parasite's feeding strategy affects both parasite requirements of the host environment and parasite impacts on the host environment. We hypothesized that parasites that more strongly modify niches available within a host will be associated with greater changes in microbiome diversity and composition. Parasites with a feeding strategy that creates necrotic tissue to extract resources (necrotrophs) may not only have different niche requirements, but also act as particularly strong niche modifiers. Barcoded amplicon sequencing of the fungal ITS region revealed that leaf segments symptomatic of necrotrophs had lower fungal diversity and distinct composition compared to segments that were asymptomatic or symptomatic of other parasites. There were no clear differences in fungal diversity or composition between leaf segments that were asymptomatic and segments symptomatic of other parasite feeding strategies. Our results motivate future experimental work to test how the relationship between the microbiome and parasite infection is impacted by parasite feeding strategy and highlight the potential importance of parasite traits.

Culturable root endophyte communities are shaped by both warming and plant host identity in the Rocky Mountains, USA

Abstract Understanding the biogeographic patterns of root-associated fungi and their sensitivity to temperature may improve predictions of future changes in terrestrial biodiversity and associated ecosystem processes, but data are currently limited. Anticipating change will require combining observational data, which predict how climatic factors limit current species distributions, with direct manipulations of climate, which can isolate responses to specific climate variables. Root endophytes are common symbionts of plants, particularly in arctic and alpine environments, yet their responses to climate warming are not resolved. Here, we directly cultured endophytic fungi from roots collected along altitudinal gradients in replicated mountain watersheds and from a 27 y field warming experiment in the Rocky Mountains, USA, to improve understanding of climate impacts on fungal root endophytes. Fungal taxa that were common at high elevations declined most under climate warming, whereas low elevation dominants responded neutrally or increased with experimental warming. Altitudinal gradients in fungal communities were strongly specific to the plant host species. Specifically, Poa species had 25–60% greater fungal isolate abundance and 25–38% greater fungal diversity at high elevations than at low elevation sites. In contrast, Festuca thurberi had 64% lower fungal diversity on roots at high elevation than at low elevation. Our results help to improve understanding of the potential for climate change to alter plant-fungal interactions in mountain ecosystems.

Effects of burning and mowing on the soil microbiome of restored tallgrass prairie

AbstractUnderstanding soil microbiome responses to different land‐management strategies provides insights into tallgrass prairie restoration. However, few studies have examined these interactions. We addressed this issue by surveying samples from the University of Nebraska at Omaha's Glacier Creek Preserve, where a long‐term burn experiment was established in 1982, with the mow treatments incorporated in 2002. In 2015, we collected 89 soil samples and obtained ~2.3 million bacterial and archaeal 16S rRNA sequence reads and ~2.4 million fungal ITS reads. Analysis of the sequences showed that dominant phyla were Proteobacteria (~30.0%) and Acidobacteria (~22.8%) in bacteria and Ascomycota (~66.2%) in fungi. We found that burning and mowing had a distinct effect on soil bacterial and fungal diversity: soils exposed to the burn treatments possessed a relatively high bacterial diversity but a relatively low fungal diversity. We also observed that burning and mowing had different effects on different microbial groups within bacteria and fungi. The burn treatments led to a relatively high abundance of bacterial groups such as Gemmatimonadetes and Armatimonadetes that prefer dry or warmer soils and arbuscular mycorrhizal (AM) fungi, whereas the mow treatments resulted in increased abundances of Nitrospirae bacteria. Moreover, functional prediction revealed that soil samples from the burn treatments were enriched with AM and plant saprotrophic fungi, and fungal plant pathogens were enriched in the mow samples. Considering soil functional differences between burn and mow treatments and an increased plant production after burning treatments, we speculate that burning could be a better strategy in the tallgrass land restoration, with certain fungal groups as an imperative indicator.Highlights Understanding soil microbiome responses to different land‐management strategies provides insights into tallgrass prairie restoration We showed differences in the soil bacterial and fungal communities between burn and mow treatments. Soil fungi were enriched in AM fungi and plant saprotroph functions after burning, but fungi with putative plant pathogens after mowing. The burn treatment is a better strategy for tallgrass prairie land restoration in this study region.

Plant nutrient-acquisition strategies drive topsoil microbiome structure and function.

Plant nutrient-acquisition strategies drive soil processes and vegetation performance, but their effect on the soil microbiome remains poorly understood. This knowledge is important to predict the shifts in microbial diversity and functions due to increasing changes in vegetation traits under global change. Here we documented the topsoil microbiomes of 145 boreal and temperate terrestrial sites in the Baltic region that broadly differed in vegetation type and nutritional traits, such as mycorrhizal types and symbiotic nitrogen-fixation. We found that sites dominated by arbuscular mycorrhizal (AM) vegetation harbor relatively more AM fungi, bacteria, fungal saprotrophs, and pathogens in the topsoil compared with sites dominated by ectomycorrhizal (EM) plants. These differences in microbiome composition reflect the rapid nutrient cycling and negative plant-soil feedback in AM soils. Lower fungal diversity and bacteria:fungi ratios in EM-dominated habitats are driven by monodominance of woody vegetation as well as soil acidification by EM fungi, which are associated with greater diversity and relative abundance of carbohydrate-active enzymes. Our study suggests that shifts in vegetation related to global change and land use may strongly alter the topsoil microbiome structure and function.

Contrasting microbiomes of raw and ripened Pu-erh tea associated with distinct chemical profiles

Pu-erh tea has become one of the popular and widely consumed teas because of its health benefits resulted from various bioactive compounds that are microbially produced during Pu-erh tea production. We applied 16S rRNA gene amplicon sequencing and analytical tools to investigate microbiomes and associated chemical profiles of five raw and five ripened Pu-erh teas from different manufacturers. Contrasting bacterial and fungal microbiomes of raw and ripened Pu-erh tea samples associated with distinct chemical profiles were revealed. The ripened Pu-erh teas had a higher bacterial diversity but lower fungal diversity than the raw Pu-erh teas. Firmicutes and Proteobacteria were the dominant phyla in the ripened and raw Pu-erh tea, respectively. Cyanobacteria phylum was found very abundant in the raw but rarely present in the ripened Pu-erh tea. Ascomycota was the dominant fungal phylum in both ripened and raw Pu-erh tea. Tea polysaccharide and gallocatechin gallate were the characteristic chemicals in the ripened Pu-erh tea; while caffeic acid, caffeine, EGC, ECG, EGCG, C, and GA were more representative in the raw Pu-erh tea. These results will assist in further cultivating and characterizing the representative microorganisms in Pu-erh teas of different origins, and improve our understanding of microbial-mediated Pu-erh tea production process.

Maize (Zea mays L. Sp.) varieties significantly influence bacterial and fungal community in bulk soil, rhizosphere soil and phyllosphere.

The plant-microbe interaction can affect ecosystem function, and many studies have demonstrated that plant species influence relevant microorganisms. In this study, microbial communities in bulk soil, rhizosphere soil and phyllosphere from different maize varieties were investigated using high-throughput sequencing method. Results demonstrated that cultivar Gaoneng 1 (G1) showed higher bacterial diversity in soil (both bulk and rhizosphere soils) and lower bacterial diversity in the phyllosphere, while cultivar Gaoneng 2 (G2) had lower fungal diversity in both the soil and phyllosphere compare to the other cultivars. The bacterial community structure of soils among the three varieties was significantly different; however, no significant differences were found in the soil fungal community and phyllosphere bacterial and fungal community. The soil networks from cultivar G1 and phyllosphere networks from cultivar Zhengdan (ZD) have the highest complexity in contrast to the other two cultivars. In conclusion, the bacterial community structure in bulk soil of different cultivars was significantly different, so do the co-occurrence ecological networks of phyllosphere bacterial community. This study comprehensively analyzed the microbial community among different maize cultivars and could be useful for guiding practices, such as evaluation of new plant cultivars and quality predictions of these varieties at the microbial level.

Impact of Gut Mycobiota Composition on Outcomes after Allogeneic Hematopoietic Cell Transplantation

Alterations of gut bacterial microbiota composition have been associated with outcome after allogeneic hematopoietic cell transplantation (alloHCT), including overall survival (OS), graft versus host disease (GVHD) and relapse incidence . Furthermore, the role of eukaryotic gut virome in GVHD was recently shown (Legoff et al., Nature Medicine, 2017). In contrast, the impact of gut fungal microbiota (mycobiota) is still unknown in the alloHCT setting. Earlier studies in patients with inflammatory bowel diseases or primary sclerosing cholangitis, suggested that gut mycobiota composition and diversity contribute to disease severity. With this background, we examined the role of fecal mycobiota in patients undergoing alloHCT with the aim of identifying fungi factors associated with patients' outcome. Fecal specimens were collected at day 0 of alloHCT (before graft infusion). The fecal mycobioat was characterized by ITS2 sequencing using the MiSeq (illumine) technology. Phylogenetic classification was obtained using the UNITE ITS database (version 12_11). Association of fungal microbiota with clinical predictors and outcomes were assessed using multivariate modeling. In all, we analyzed 52 patients (28 males and 24 females). Median age was 60 (range, 22-74) years. Disease risk index was low-intermediate in 29 patients, high-very high in 20 patients (not assessed in 3 patients with aplastic anemia). Fourty three patients received a myeloablative reduced toxicity conditioning regimen, while 9 patients received a reduced intensity conditioning regimen. Ten patients received their graft from a matched sibling donor, 11 from a haploidentical donor, and 26 from a matched or mismatched unrelated donor. All patients received anti-thymocyte globulin as part of their conditioning regimen, and patients undergoing alloHCT from a haploidentical donor also received post-transplant cyclophosphamide. Overall we found a low fungal diversity score of the fungal microbiota at day 0 in all patients from this cohort, with little variations. Therefore, it proved difficult to establish any statistically significant correlations between fungal diversity and patients outcome. However, in multivariate Cox hazard analysis including the most important parameters associated with patients' outcome, we found that an increased proportion (&amp;gt;median) of Candida albicans and Malassezia genera was associated with a lower OS [Hazard ratio (HR)= 7.12, p=0.02 and HR=14.99, p=0.007, respectively]. We did not find any parameter with a significant impact on progression free survival in multivariate analysis. When investigating acute GVHD, a hight amount of Candida glabrata (&amp;gt;median) was the only parameter associated with grade II-IV acute GVHD in multivariate analysis (HR=4.49, p=0.009). The day 180 cumulative incidence of grade II-IV acute GVHD was 24% in patients with low Candida glabrata colonization (below the median) versus 80% (p=0.0005) in patients with high Candida glabrata colonization (above the median). In conclusion, we found an important disruption of the fecal mycobiota in patients undergoing alloHCT, as evidenced by the low fungal diversity observed at day 0 . Furthermore, increased amount of Candida albicans and Malassezia genera at the time of alloHCT were independent predictors of mortality. Finally fecal mycobiota might also contribute to acute GVHD as evidenced by the higher incidence of grade II-IV acute GVHD in patients colonized with higher amount of Candida glabrata . These results indicate that, in addition to bacterial and viral microbiota, the mycobiota might be an important factor influencing outcome after alloHCT. Disclosures Malard: Therakos/Mallinckrodt: Honoraria; Janssen: Honoraria; Keocyte: Honoraria; Sanofi: Honoraria; JAZZ pharmaceutical: Honoraria; Astellas: Honoraria. Duléry:Keocyt: Honoraria. Mohty:Jazz Pharmaceuticals: Honoraria, Research Funding.

Review article: fungal alterations in inflammatory bowel diseases.

Emerging data suggest that alterations in gut fungi may be associated with the pathogenesis of inflammatory bowel disease (IBD). In healthy individuals, gut commensal fungi act synergistically with other members of the microbiota to maintain homeostasis but their role in IBD is less clear. To review the role of gut fungi and their trans-kingdom interactions with bacteria in IBD METHODS: A literature search was conducted on Ovid and Pubmed to select relevant animal and human studies that have reported fungi and IBD. There is an increased total fungal load particularly of Candida and Malassezia species in the faeces and mucosa of Crohn's disease patients, and a lower fungal diversity in the faeces of ulcerative colitis patients. Caspase recruitment domain-containing protein (CARD)-9 polymorphism in Crohn's disease patients favours Malassezia colonisation that worsens gut inflammation. Diet high in carbohydrates increased the total abundance of Candida species, whereas protein-rich diet had the opposite effect. Anti-fungal therapies are mostly used to treat Candida albicans or Histoplasma capsulatum infections in IBD, whereas pilot studies of supplementing fungal probiotics Saccharomycopsis fibuligera, Saccharomyces boulardii and Saccharomyces cerevisiae CNCM I-3856 strain showed therapeutic effects in IBD. Gut fungi are altered in patients with Crohn's disease and ulcerative colitis. Modulation of the fungal microbiota can be considered as a therapeutic approach for IBD. Future research should focus on understanding how the fungal microbiota interacts with other components of the gut microbiota in association with the pathogenesis and development of IBD.