Fungal Communities Research Articles

Future climate and agricultural farming systems affect the fungal plastisphere of different biodegradable plastics at the early stage of field degradation

BackgroundThe use of biodegradable mulch films has an advantage over non-biodegradable ones, as it offers degradation by microbes under environmental conditions. Nevertheless, less is known about the microbial colonization of different biodegradable plastics under different agricultural systems and climate change conditions. In the current study, the plastic degradation experiment was conducted at the Global Change Experimental Facility platform, specifically in conventional and organic farming systems, both under ambient and future climatic conditions. In this study, we investigated the early fungal colonizers associated with polybutylene-succinate (PBS) and polybutylene adipate-co-terephthalate (PBAT) with polyethylene (PE) as a reference in comparison to the initial soil fungal community.ResultsWe found a distinct pattern between soil and plastisphere fungi. Soil fungi were dominated by Sordariomycetes (mainly Gibellulopsis, Fusarium, and Gibberella), and fungi in plastics were dominated by Dothideomycetes (mainly Mycosphaerella, Alternaria, and Cladosporium). These microbes were previously reported as plastic colonizers and potential plastic degraders. We found that agricultural systems affect both fungal richness and community composition of the plastisphere. Plastic type significantly affected the fungal richness, but not the fungal community composition. The two different agricultural systems undergo different treatments, including crop rotation and fertilization, which in turn impact the fungal colonization of the biodegradable plastics.ConclusionsThis study provides new insights into factors that affect early fungal colonization of different biodegradable plastics under real field conditions using high-throughput sequencing. These data are of high relevance to evaluate the plastic composition for adjusted rate of plastic biodegradation for upcoming mulch film products.

Unraveling the Rhubarb (Rheum officinale Baill.) Root and Rhizosphere Microbial Communities in Response to Pathogen Exposure.

This study investigated the microbial community composition and structure in healthy and diseased rhubarb (Rheum rhabarbarum) root systems, examining both root tissue and rhizosphere environments. Alpha diversity analysis revealed significantly higher microbial abundance in the rhizosphere compared to root tissues, with notable differences between healthy and diseased plants. Principal coordinate analysis demonstrated that bacterial community composition was primarily influenced by ecological niches (47.5% variation explained), whereas fungal communities segregated based on plant health status. Network analysis revealed increased bacterial community complexity in diseased plants rhizosphere (579 nodes, 13,016 edges) compared to healthy plants (542 nodes, 8700 edges), while fungal networks showed opposite trends with significant reduction in diseased conditions (147 nodes, 30 edges vs. 205 nodes, 418 edges). Correlation analysis identified significant associations between specific microbial taxa and soil properties, with notable positive correlations between certain bacteria (Oscillospirales) and fungi (Barnettozyma, Mortierella) with soil organic matter and nutrient availability. Pathogenic taxa, including Fusarium and members of Burkholderiales, showed negative correlations with beneficial microorganisms, suggesting potential antagonistic relationships. These findings provide crucial insights into the complex interactions within the rhubarb root microbiome and their implications for plant health, contributing to our understanding of root rot disease dynamics and potential management strategies.

Small-scale fire refugia increase soil bacterial and fungal richness and increase community cohesion nine years after fire.

Small-scale variation in wildfire behavior may cause large differences in belowground bacterial and fungal communities with consequences for belowground microbial diversity, community assembly, and function. Here we combine pre-fire, active-fire, and post-wildfire measurements in a mixed-conifer forest to identify how fine-scale wildfire behavior, unburned refugia, and aboveground forest structure are associated with belowground bacterial and fungal communities nine years after wildfire. We used fine-scale mapping of small (0.9-172.6m2) refugia to sample soil-associated burned and refugial microbial communities. Richness was higher in refugia for bacteria (+19%) and fungi (+31%) and in all functional guilds relative to burned soils. Refugial communities had greater proportions of saprotrophic and lower proportions of pathogenic fungi relative to burned soils. Composition differed in burned areas and refugia and was most strongly associated with small-scale fire behavior, aboveground live tree basal area, and tree mortality. Refugial communities had more connected association networks and fewer facilitative interactions relative to burned soils - supporting both the stress-gradient hypothesis and the conclusion that refugial communities may have greater resistance to future disturbance. Small-scale differences in wildfire behavior and effects can have long-term impacts on belowground microbes, highlighting the need to assess neighborhood effects at spatial scales that influence microbes.

Correction: Loiko, N.; Islam, M.N. Plant–Soil Microbial Interaction: Differential Adaptations of Beneficial vs. Pathogenic Bacterial and Fungal Communities to Climate-Induced Drought. Agronomy 2024, 14, 1949

Correction: Loiko, N.; Islam, M.N. Plant–Soil Microbial Interaction: Differential Adaptations of Beneficial vs. Pathogenic Bacterial and Fungal Communities to Climate-Induced Drought. Agronomy 2024, 14, 1949

Structure and assembly of fungal communities in the phyllosphere and endosphere of healthy and diseased faba bean plants

Structure and assembly of fungal communities in the phyllosphere and endosphere of healthy and diseased faba bean plants

Bacterial and Fungal Communities Respond Differently to Changing Soil Properties Along Afforestation Dynamic

Spontaneous afforestation following land abandonment has been increasingly recognized as a nature-based solution to mitigate climate change and provide measurable benefits to biodiversity. However, afforestation effects on biodiversity, particularly on soil microbial communities, are still poorly characterized, with most previous studies focusing on artificial plantations rather than forest rewilding dynamics. Here, we assessed changes in topsoil physical–chemical properties and related dynamics of bacterial and fungal community composition and structure following spontaneous afforestation of abandoned grasslands in Northeast Italy over the last 70 years. With a space-for-time approach, we selected four chronosequences representing different successional stages: grassland, early (2000–2020), intermediate (1978–2000), and late (1954–1978). Results showed that spontaneous afforestation progressively reduced topsoil pH and total phosphorus (P), while soil organic carbon (SOC), nitrogen (N), and C:N ratio increased. Correspondingly, the overall α-diversity of the fungal community, assessed by ITS DNA metabarcoding, progressively decreased after an initial increase from grassland conditions, following substrate acidification and trophic specialization. Bacterial diversity, assessed by 16S DNA metabarcoding, was highest at the initial stages, then progressively decreased at later stages, likely limited by lower organic matter quality. Shifts of fungal community composition included an increase of ectomycorrhizal Basidiomycota linked to topsoil’s higher SOC, N, and C:N ratio. Differently, bacterial community composition responded substantially to pH, with topsoil acidity favoring Proteobacteria (Pseudomonadota) and Acidobacteria (Acidobacteriota) at the late afforestation stages. Our findings provide a first contribution to clarify how fungi and bacteria respond to spontaneous afforestation. This is particularly relevant in the context of climate change mitigation, considering the fundamental role of microorganisms in shaping soil carbon storage dynamics.

Effects of Nitrogen Addition and Drought on Soil Microbial Diversity and Community Composition in a Young Tree Community

Soil microorganisms are well known to play a crucial role in carbon and nutrient cycling within terrestrial ecosystems. Numerous research efforts have demonstrated that nitrogen deposition can change forest soil microbial diversity and community composition; however, it is still unclear how nitrogen deposition will affect the soil microbial diversity and community composition in subtropical forests under the background of increasing drought. Consequently, over a period of 2.5 years, we carried out an experiment using two N addition regimes and three soil water treatment levels to reveal the effects of nitrogen, drought, and the influence of their interaction on the diversity and community composition of soil microorganisms. Overall, we found that both N addition and drought decreased the bacterial Shannon and Simpson indices yet had no significant effect on fungal diversity. In the well-watered treatments, nitrogen addition did not significantly reduce bacterial diversity, while in the moderate drought and severe drought treatments, N addition significantly decreased bacterial diversity, reducing the Shannon and Simpson indices by 27.05% and 0.13%, respectively, in the severe drought treatment. Drought significantly altered the community composition of bacteria regardless of N addition. N addition significantly changed the community composition of bacteria under moderate drought treatments, while both N addition and drought had less significant effects on the fungal community composition. The soil water content, fine root biomass, and soil pH were significantly correlated with bacterial community composition, which explained 53.3%, 11.1%, and 8.7% of the changes in soil bacterial community composition, respectively. These results suggest that drought may intensify the inhibitory effect of nitrogen on bacterial diversity and change the magnitude and direction of the impact of nitrogen on the composition of the bacterial community.

Contrasting fungal community assembly mechanisms in bulk soil and rhizosphere of Torreya grandis across a 900-year age gradient

Contrasting fungal community assembly mechanisms in bulk soil and rhizosphere of Torreya grandis across a 900-year age gradient

Impacts of pseudomonas fluorescent bacterial fertilizer addition on the soil environment and fruit yield under water stress in greenhouse grape

Bacterial fertilizers, which contain beneficial soil microorganisms, are becoming more widely used as they can mitigate the problems of crop yields reduction and soil environment degradation caused by the overuse of chemical fertilizer. However, the impact of bacterial fertilizer on greenhouse grape yields and the rhizosphere soil environment has not been assessed in arid and semi-arid region of Northwest China. Thus, a 2-year field trial was conducted with five treatments: adequate water supply without bacterial fertilizer (CK); mild (W1), moderate (W2) water stress and small (F1), maximize (F2) fertilizer cross-combination, respectively. The results indicated that water stress had a negative impact on the accumulation of dissolved organic carbon (DOC), microbial biomass carbon (MBC), and microbial biomass nitrogen (MBN) in the rhizosphere soil. The addition of pseudomonas fluorescent bacterial fertilizer significantly increased the content of available phosphorus (AP), DOC, MBC and MBN content. The W1F2 treatment significantly increased the activities of urease, catalase and sucrase (p < 0.05). The W1F1 and W1F2 treatments increased fungal and bacterial diversity. Bacterial community composition was closely related to soil total organic carbon (TOC), soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), MBC, and sucrase, while fungi community composition was significantly related to Nitrate-N (NO3−-N), TN, and sucrase. Additionally, compared with CK treatment the yield and economic benefit of the W1F2 treatment increased by 35.44 and 44.04%, respectively. Therefore, W1F2 is recommended as the optimal water and fertilizer management scheme for efficient greenhouse grape production in the arid and semi-arid region of Northwest China.

Seed endophytes of malting barley from different locations are shaped differently and are associated with malt quality traits

Maximizing microbial functions for improving crop performance requires better understanding of the important drivers of plant-associated microbiomes. However, it remains unclear the forces that shapes microbial structure and assembly, and how plant seed-microbiome interactions impact grain quality. In this work, we characterized the seed endophytic microbial communities of malting barley from different geographical locations and investigated associations between microbial (bacterial and fungal) species diversity and malt quality traits. Host genotype, location, and interactions (genotype x location) significantly impacted the seed endophytic microbial communities. Taxonomic composition analysis identified the most abundant genera for bacterial and fungal communities to be Bacillus (belonging to phylum Firmicutes) and Blumeria (belonging to phylum Ascomycota), respectively. We observed that a greater proportion of bacterial amplicon sequence variants (bacterial ASVs) were shared across genotypes and across locations while the greater proportion of the fungal ASVs were unique to each genotype and location. Association analysis showed a significant negative correlation between bacterial alpha diversity indices (Faith PD and Shannon indices) and malt quality traits for barley protein (BP), free amino nitrogen (FAN), diastatic power (DP) and alpha amylase (AA), while fungal alpha diversity (Shannon and Simpson) showed significant negative relationship with β-D-glucan content. In addition, some bacterial and fungal genera were significantly associated with malt extract (ME) -a key trait for maltsters and brewers. We conclude that barley genotype, location, and their interactions shape the seed endophytic microbiome and is key to microbiome manipulation and management during barley production and/or malting.

Pathogenic Fungi Communities in Contrasted Yam Field Soils are Dominated by The Genus Fusarium in Centre Côte d’Ivoire

Below-ground pathogenic fungi of yam, a globally important food crop are shown to be responsible of field and storage diseases and as such are important threats to yam health. However, yam soil pathogenic fungi community composition and soil determinants remain unclear. Here, we explored the effects of soil physicochemical characteristics on soil fungal phytopathogens in contrasted yam fields. Illumina miseq was used to characterize pathogenic fungi communities in yam field soils. In this work, we hypothesise that pathogenic community composition could be linked to specific physicochemical properties within yam contrasted soils. Principal Coordinate Analysis (PCoA) and variance partitioning were used to identify the soil properties that significantly influence pathogenic fungi community compositions within the three sites in a yam production zone. The results have shown that despite the fact that the three sites exhibited contrasted soils grouped in two types according to physicochemical parameters, four ubiquitous genera including Fusarium, Penicillium, Aspergillus and Trichoderma were identified within pathogenic fungi communities in yam field soils, with Fusarium as the most dominant core genus. Soil type determined the distribution of pathogenic fungi communities in yam field soils, and this effect was attributed to soil properties related to yam soil cation exchange capacity (CEC) and silt content as well as three micronutrients including Na, N and total phosphorus.

Correlating Feed Efficiency with Ruminal Bacterial, Fungal, and Archaeal Community Composition in Dairy Cows over Two Lactations

Dairy cows rely on their complex rumen microbial community to convert host-indigestible feed into nutrients usable for host growth, maintenance, and milk production. Previous work by our group found that the rumen bacterial community is dynamic over the course of two lactations and that cows with high and low milk production efficiency (MPE) have different taxa associated with either phenotype. Here, we characterized the ruminal fungal and archaeal communities to determine if these microbial populations exhibit properties similar to that of the rumen bacteria with respect to MPE over time. Our results show a decrease in fungal diversity over the course of both lactation cycles with an increase during the transition period. The fungal community had only a few taxa associated with efficiency. For the ruminal archaea, we found no change in diversity across both lactation cycles and only taxa in the genus Methanospera were found to be more abundant in high-MPE cows. Given that our previous study used 454 pyrosequencing, we also sought to determine if a resequencing of these communities using Illumina-based technology would alter our previous findings. We found that resequencing showed no significant deviation from our original broad conclusions, with the exception of some minor taxonomic associations.

Desiccation as a suitable alternative to cold-storage of phyllosphere samples for DNA-based microbial community analyses.

The study of microbial communities of the plant phyllosphere in remote locations using DNA-based approaches is limited by the challenges associated with their preservation in the field and during transportation. Freezing is a common DNA preservation strategy, but it may be unsuitable for leaf samples, or inaccessible in some locations. Other methods such as desiccation, ethanol or commercial preservatives are potential alternative DNA preservation methods for ambient temperature storage. In this study, we assessed the efficacy of desiccation (with silica gel packs), and of three preservation solutions (95% ethanol, RNAlater, LifeGuard) for the preservation of epiphytic phyllosphere communities of Populus tremuloides and Picea glauca at ambient indoor temperature (21°C) for up to three weeks. We assessed effects on DNA concentration and quality and used metabarcoding to detect changes in bacterial and fungal communities between treatments over time. A secondary study was conducted on leaves of Populus grandidentata to further test the ability of the desiccation treatment to resolve differences between sampling sites. Silica gel packs were identified as effective ambient temperature preservative of phyllosphere bacterial and fungal communities. There were some changes in the communities compared to immediate extraction due to this treatment, but these changes did not affect the ability to distinguish tree species and sampling locations. Overall, our study supports the use of silica gel pack short term preservation at ambient temperature for phyllosphere samples intended for DNA-based microbial community analyses.

Digging deeper into the impacts of different soil water systems on the date palm root architecture and associated fungal communities

Abstract In arid regions, excessive water use threatens agricultural sustainability and overall livelihoods. It is essential to minimize water consumption to address these issues. Date palm (Phoenix dactylifera L.) is an emblematic crop of arid regions and a major water consumer. Adapting current irrigation systems to be more water-efficient systems could help cope with the water consumption of this crop. Microbial communities associated with plants are essential for agricultural sustainability and could improve the water use efficiency in regions threatened by water scarcity. These communities should thus be seriously taken into account when adapting agrosystems to the current global change setting. However, no information is presently available on the effects of the different soil water systems on date palm microbial communities. This study highlights the impact of different soil water systems (flooding and drip irrigation, natural conditions and abandoned farms) on date palm root fungal communities at different soil depths (40, 80 and 140 cm deep). The findings revealed that the soil water systems had a marked impact on fungal communities and that drip irrigation reduced the fungal diversity but increased the abundance of arbuscular mycorrhizal fungi. We showed that these effects were similar at all sampling depths. Finally, as the root architecture is a major determinant of water uptake, we reveal different behaviors of the root architecture under these different soil water systems to 160 cm depth. The findings of this study give new insights into the date palm root architecture and associated fungal communities, particularly in the context of the water availability crisis, which drives the adaptation of agricultural systems.

Cultivation of Genetically Modified Soybeans Did Not Alter the Overall Structure of Rhizosphere Soil Microbial Communities

Herbicide-tolerant soybeans are the most extensively cultivated genetically modified (GM) crop globally. The effects of GM soybean and associated agronomic practices on soil microbial communities remain poorly understood. This study aimed to investigate the impact of planting GM soybeans with a glyphosate application on soil microbial diversity. The main bacterial and fungal community compositions (phylum level) were consistent for GM and non-GM soybeans. The alpha diversity analysis indicated that the bacterial Shannon index was significantly higher in GM rhizosphere soil during flowering compared to non-GM soil. There were no significant differences in the Shannon, Simpson, or ACE indices of the soil fungal communities between GM and non-GM soybeans in the same period. The PCoA analysis showed no significant differences in community structure between the GM and non-GM soybean soil for either fungi or bacteria during the same period. Although the relative abundance of Bradyrhizobium at the seedling stage was significantly lower in those GM than in those non-GM, it did not affect the final number of root nodules in either soybean type. The relative abundance of Frankia was significantly lower in GM rhizosphere soil during the seedling and flowering stages, whereas that of Thelebolus was significantly higher during flowering and pod filling. The abundance and ecological functions of these taxa warrant continuous monitoring.

Wind Is a Primary Driver of Fungal Dispersal Across a Mainland-Island System.

Dispersal is one of the main processes shaping ecological communities. Yet, for species-rich communities in natural systems, the role of dispersal in community assembly remains relatively less studied compared to other processes. This is the case for fungal communities, for which predictable knowledge about where and how the dispersal propagules move across space is largely lacking. We sampled fungal communities at their dispersal stage in a lake mainland-island system in Finland, using a regular grid of 18 × 18 km, including sites on the mainland, islands and over the water. Fungal communities were screened by applying DNA barcoding to air samples. To assess the factors determining fungal dispersal, we modelled aerial fungal communities with a joint species distribution model, including spore traits, weather-related predictors, and spatial predictors. We found that the probability of occurrence of most species (and consequently species richness measured as the number of OTUs per sample) was lower in low-connectivity sites (water and isolated islands) compared to high-connectivity sites (mainland). There was a strong phylogenetic signal in how the fungal species responded to connectivity, indicating that some taxonomic groups are more dispersal limited than others, although such responses were not structured by their trophic guilds. Furthermore, wind speed influenced how species with different spore sizes responded to connectivity: in low-connectivity sites, species with large sexual spores were detected especially when wind was high, whereas, in high-connectivity sites, they were detected especially when wind was low. This study demonstrates that air fungal dispersal might be more predictable than previously considered and contributes to the mechanistic understanding of fungal air dispersal.

Both light and soil moisture affect the rhizosphere microecology in two oak species

Understanding the mechanisms by which seedlings respond to light and water regulation, as well as studying the response of rhizosphere microecology to drought stress, are crucial for forest ecosystem management and ecological restoration. To elucidate the response of the rhizosphere microecology of Quercus dentata and Quercus variabilis seedlings to water and light conditions, and to clarify how plants modulate the structure and function of rhizosphere microbial communities under drought stress, we conducted 12 water-light gradient control experiments. These experiments aimed to offer scientific theoretical support for the dynamic changes in rhizosphere soil enzyme activities and microbial community compositions of these two oak species under varying light and moisture conditions, and subsequently assist in the future breeding and cultivation efforts. The results are summarized as follows: (1) The activities of cellulase, urease, and chitinase in the rhizosphere soil of Q. dentata and Q. variabilis were significantly influenced by water and light treatments (p < 0.05). Urease was particularly sensitive to light, while sucrase exhibited sensitivity to light in Q. dentata and no significant difference in Q. variabilis. (2) Compared to Q. dentata, the rhizosphere bacteria of Q. variabilis demonstrated greater adaptability to drought conditions. Significant differences were observed in the composition of microorganisms and types of fungi in the rhizosphere soil of the two Quercus seedlings. The fungal community is significantly influenced by light and moisture, and appropriate shading treatment can increase the species diversity of fungi; (3) Under different water and light treatments, the rhizosphere soil microbial composition and dominant species differed significantly between the two Quercus seedlings. For instance, Streptomyces, Mesorhizobium, and Paecilomyces exhibited significant variations under different treatment conditions. Specifically, under L3W0 (25% light, 75–85% moisture) conditions, Hyphomonadaceae and SWB02 dominated in the Q. dentata rhizosphere, whereas Burkholderiales and Nitrosomonadaceae were prevalent in the Q. variabilis rhizosphere. Overall, the rhizosphere microecology of Q. dentata and Q. variabilis exhibited markedly distinct responses to varying light and water regimen conditions. Under identical conditions, however, the enzyme activity and microbial community composition in the rhizosphere soil of these two oak seedlings were found to be similar.

Seasonal variation of airborne fungal diversity and community structure in Urmia Lake, Iran.

A study conducted around Urmia Lake, Iran, investigated the impact of dust storms on fungal concentrations in the air. Researchers collected samples over a year, analyzing fungal variations during dusty and normal days. The average fungal concentration was found to be 436.2 CFU/m3, with Cladosporium cladosporioides, Penicillium chrysogenum, and Cladosporium iridis being the most prevalent species. Notably, fungal concentrations during dust days averaged 967.65 CFU/m3, which is 3.6 times higher than on normal days (267.10 CFU/m3). A total of 61 species were detected on normal days, compared to 45 on dusty days, with Aspergillus and Cladosporium spp. dominating both conditions. The study also linked environmental factors like temperature, humidity, and wind speed to fungal concentrations. Additionally, the distribution of dust was analyzed using the HYSPLIT model and MODIS satellite imagery, highlighting the health risks associated with high fungal concentrations and changing mycobiota due to dust disturbances.

A novel decomposer-exploiter interaction framework of plant residue microbial decomposition

BackgroundPlant residue microbial decomposition, subject to significant environmental regulation, represents a crucial ecological process shaping and cycling the largest terrestrial soil organic carbon pool. However, the fundamental understanding of the functional dynamics and interactions between the principal participants, fungi and bacteria, in natural habitats remains limited.ResultsIn this study, the evolution of fungal and bacterial communities and their functional interactions were elucidated during the degradation of complexity-gradient plant residues. The results reveal that with increasing residue complexity, fungi exhibit heightened adaptability, while bacterial richness declines sharply. The differential functional evolution of fungi and bacteria is driven by residue complexity but follows distinct trajectories. Fundamentally, fungi evolve towards promoting plant residue degradation and so consistently act as the dominant decomposers. Conversely, bacteria predominantly increase expression of genes of glycosidases to exploit fungal degradation products, thereby consistently acting as exploiters. The presence of fungi enables and endures bacterial exploitation.ConclusionsThis study introduces a novel framework of fungal decomposers and bacterial exploiters during plant residue microbial decomposition, advancing our comprehensive understanding of microbial processes governing the organic carbon cycling.

The application of shrub willow chip organic amendments impacts soil microbial community dynamics.

Incorporating shrub willow chips into soil may improve the chemical, physical and biological properties of soils with low organic matter but the impact on soil microbial communities and their dynamics is not known. We assessed changes in the soil microbial communities in response to willow chip applied at increasing rates (0, 20, 40 and 60 Mg ha-1) in a potato-barley cropping system. Bacterial and fungal community diversity, relative abundance, and potential functions were assessed using amplicon sequencing of 16S and ITS rRNA genes at six time points. High rates (40 and 60 Mg ha-1) of willow chips had no effect on bacterial alpha diversity but significantly decreased fungal alpha diversity (Shannon) while increasing fungal richness (Chao-1). At rates of 40 Mg ha⁻¹ and higher, the relative abundance of copiotrophic bacterial groups increased, while that of copiotrophic fungal groups decreased. The relative abundance of the most dominant microbial phyla and genera varied over time, with copiotrophic groups declining and oligotrophic groups increasing. High willow chip application rates increased bacterial molecular markers related to carbon fixation and degradation, nitrogen fixation, and phosphorus solubilization, while decreasing markers related to cellobiose transport and denitrification. This study demonstrates the ability of willow chips to influence the microbial community composition and potential function over time.