Fungal Community Structure Research Articles

Mycorrhizal and endophytic fungi structure forest below-ground symbiosis through contrasting but interdependent assembly processes

BackgroundInteractions between plants and diverse root-associated fungi are essential drivers of forest ecosystem dynamics. The symbiosis is potentially dependent on multiple ecological factors/processes such as host/symbiont specificity, background soil microbiome, inter-root dispersal of symbionts, and fungus–fungus interactions within roots. Nonetheless, it has remained a major challenge to reveal the mechanisms by which those multiple factors/processes determine the assembly of root-associated fungal communities. Based on the framework of joint species distribution modeling, we examined 1,615 root-tips samples collected in a cool-temperate forest to reveal how root-associated fungal community structure was collectively formed through filtering by host plants, associations with background soil fungi, spatial autocorrelation, and symbiont–symbiont interactions. In addition, to detect fungi that drive the assembly of the entire root-associated fungal community, we inferred networks of direct fungus–fungus associations by a statistical modeling that could account for implicit environmental effects.ResultsThe fine-scale community structure of root-associated fungi were best explained by the statistical model including the four ecological factors/processes. Meanwhile, among partial models, those including background soil fungal community structure and within-root fungus–fungus interactions showed the highest performance. When fine-root distributions were examined, ectomycorrhizal fungi tended to show stronger associations with background soil community structure and spatially autocorrelated patterns than other fungal guilds. In contrast, the distributions of root-endophytic fungi were inferred to depend greatly on fungus–fungus interactions. An additional statistical analysis further suggested that some endophytic fungi, such as Phialocephala and Leptodontidium, were placed at the core positions within the web of direct associations with other root-associated fungi.ConclusionBy applying emerging statistical frameworks to intensive datasets of root-associated fungal communities, we demonstrated background soil fungal community structure and fungus–fungus associations within roots, as well as filtering by host plants and spatial autocorrelation in ecological processes, could collectively drive the assembly of root-associated fungi. We also found that basic assembly rules could differ between mycorrhizal and endophytic fungi, both of which were major components of forest ecosystems. Consequently, knowledge of how multiple ecological factors/processes differentially drive the assembly of multiple fungal guilds is indispensable for comprehensively understanding the mechanisms by which terrestrial ecosystem dynamics are organized by plant–fungal symbiosis.

Pecan-medicinal crops intercropping improved soil fertility and promoted interactions between soil microorganisms and metabolites

BackgroundPecan [Carya illinoinensis (Wangenh.) Koch] is a widely cultivated dried fruit and woody oil tree with high economic value. Continuous sole planting of pecan caused some land to lie idle and deterioration of soil conditions. Tree and medicinal crops intercropping represents an environmental-friendly and economically feasible solution to these issues. Thus, we aimed to explore the underlying mechanism by which intercropping improved soil condition by regulating the interactions of the soil microbiome and metabolome. In this study, pecans were intercropped with medicinal crops caper spurge and honeysuckle on a tree farm in China. A combined analysis of soil microbiomes and metabolomes was performed to discover the effects of intercropping on bulk and rhizosphere soils.ResultsThe results showed that intercropping improved the edaphic properties of bulk soil and promoted the growth of pecan and caper spurge. Intercropping also significantly altered the structures of both bacterial and fungal communities in bulk soil, stabilised the enrichment of nitrogen-cyclic bacteria, for instance, Bacillus, and decreased the relative abundances of plant–pathogenic fungi, for instance, Fusarium. In addition, the result of metabolomic analysis showed that intercropping promoted the synthesis of functional compounds, such as trehalose and ethanolamine, which enhanced plant disease resistance in bulk soils. Moreover, the co-occurrence networks of microbiomes and metabolomes of bulk soils revealed that Bacillus was significantly correlated with Fusarium, Alternaria, and trehalose under intercropping patterns. Furthermore, analysis of microbiomes and metabolomes in the rhizosphere soil of caper spurge and honeysuckle revealed that Penicillium and Rhizomicrobium were significantly increased by intercropping and showed more dynamic connections with other genera and metabolites compared with single planting.ConclusionsOverall, intercropping pecans with caper spurge and honeysuckle can improve soil conditions and promote plant growth through microbiological and metabolomics integrated analyses. This study provides valuable information and theoretical basis for optimizing land resource utilisation and improving soil conditions in tree fields like pecan fields via intercropping, thereby reducing production losses and ensuring economic benefits.Graphical

Fungal Footprints: Soil Fungal Communities in Black Walnut and Red Oak Forests

Soil fungal communities are critical for forest ecosystem functions in the Central Hardwood Region (CHR) of the USA. This evaluation, which took place in 2022–2023, investigates the influence of Juglans nigra (BW, black walnut) and Quercus rubra (NRO, Northern red oak) on soil properties and fungal community structures across three CHR sites. The objectives of this study are to investigate how the fungal communities identified beneath J. nigra and Q. rubra serve to influence biodiversity and soil health within hardwood plantations. Soils from two locations in Indiana and one in Michigan were examined and assessed for variations in fungal composition and diversity. Soil fungal communities were characterized using Illumina high-throughput sequencing while multivariate analysis was applied to analyze patterns in these fungal communities. These data provided insights into how environment, location, and tree species affect fungal community structure. Results indicate that J. nigra soils exhibited higher carbon (0.36%, 1.02%, 0.72%), nitrogen (25%, 29%, 56%), and pH (0.46, 1.08, 1.54) levels than Q. rubra soils across all three sites and foster greater fungal diversity. Specifically, J. nigra was associated with increased Ascomycota diversity, whereas Q. rubra supported a higher prevalence of Basidiomycota. Basidiomycota were negatively correlated with carbon and pH, while Ascomycota showed positive correlations with these variables. These findings highlight how crucial it is to understand how different tree species influence fungal communities and, consequently, how they influence forest soil health. Our findings serve to improve forest management practices by emphasizing the importance of fungal communities in maintaining the function and resilience of an ecosystem. Our study underscores that grasping these specific interactions is essential for effective forest management, especially when considering how to use fungal communities to boost plant growth. This work focuses on hardwood plantations rather than either agricultural ecosystems, monocultures, or native forests, thus filling a gap in the current literature where many studies are limited to specific fungal groups such as mycorrhizae. In future research, it is important to examine a wider range of tree species. This will deepen our understanding of fungal community dynamics and their impact on maintaining healthy forest ecosystems. Our hardwood plantation focus also notes the potential for adaptive forest management as environmental conditions change.

Analysis of Physicochemical Properties, Enzyme Activity, Microbial Diversity in Rhizosphere Soil of Coconut (Cocos nucifera L.) Under Organic and Chemical Fertilizers, Irrigation Conditions

The application of chemical fertilizers and organic fertilizers, as well as irrigation, is an important agricultural practice that can increase crop yields and affect soil biogeochemical cycles. This study conducted coconut field experiments to investigate the effects of conventional fertilization (NCF), optimized fertilization (MCF), conventional fertilization + organic fertilizer (NOF), optimized fertilization + organic fertilizer (MOF), conventional fertilization + organic fertilizer + irrigation (NOFW), and optimized fertilization + organic fertilizer + irrigation (MOFW) treatments on soil physicochemical properties, soil enzyme activity, bacterial and fungal community structure and diversity, and compared the controls (CK, non-fertilizer and non-irrigation). The results showed that MOFW significantly increased soil electrical conductivity (EC), organic matter (OM), alkaline nitrogen (AN), available phosphorus (AP), available potassium (AK), available calcium (ACa), and available magnesium (AMg) levels. At the same time, it also significantly enhanced the activities of soil catalase (CE), polyphenol oxidase (POE), sucrase (SE), urease (UE), acid protease (APE), and acid phosphatase (APPE) (p < 0.05). The PCA analysis of soil microorganisms in the coconut rhizosphere soil showed indicated significant changes in bacteria and fungi community structure under fertilization treatments. The fertilization application leaded to an increase in the relative abundance and diversity of bacteria, but a decrease in fungi. Acidobacteriota, Proteobacteria, and Actinobacterota were the dominant bacterial phyla, and Ascomycota, Basidiomycota, Rozellomycota, and Mortierellomycota were the significant fungal phyla. Compared with CK, MOFW significantly increased the abundance of Acidobacteriota, Proteobacteria, Basidiomycota, and Mortierellomycota. Redundancy analysis (CCA) and Mantel test further revealed that pH, EC, OM, and AP were the main soil fertility factors driving changes in microbial communities. CE, SE, UE, APE, APPE were significantly correlated with microbial communities. Compared with NOFW, MOFW has a lower proportion of N, P, and K fertilizers in its fertilizer composition. The results indicated that MOFW can better improve the nutrient and enzyme status of the soil, which is a promising method for maintaining the balance of soil microorganisms in coconut orchards, and accordingly, reducing chemical fertilizers within a certain range can not only ensure consistency with conventional fertilizers, but also effectively improve soil conditions.

Short-term effects of co-applied biochar and paper mill biosolids on soil microbial communities under field conditions

Biochar and paper mill biosolids (PB) are reported to improve soil fertility, crop growth and indirectly conditions for soil microbial communities. However, it is unclear how the co-application of these materials impacts soil microbial communities under field conditions. A study was initiated in 2018 in Québec, QC, Canada and fine roots and rhizosphere soil were sampled to determine the effects of co-application of wood biochar (0, 10, and 20 Mg dry wt. ha−1) and PB (0 and 30 Mg wet wt. ha−1) on the percentage of corn (Zea mays L.) and soybean (Glycine max L. Merr.) root colonization by arbuscular mycorrhizal fungi (AMF), soil microbial biomass phosphorus (MBP) and microbial (Bacteria, Fungi and AMF) diversity and community structure in a temperate loamy soil. Co-applying PB and biochar increased soil MBP compared with the control and biochar-only application. Applying PB alone or with biochar increased the level of root colonization by AMF compared with the control and biochar-only application in soybean but not in corn. Overall, biochar and PB application had no significant effect on bacterial and AMF diversity and community structure compared with the control. However, applying PB alone or with biochar decreased the fungal alpha diversity (Shannon and Simpson indices), affected several fungal taxa abundances and shifted the fungal community structure as indicated by the principal coordination analysis (PCoA). Our results provided an understanding on the short-term effects of co-applied wood biochar and PB on microbial communities of a temperate loamy soil under field conditions, as well as scientific bases for further investigation.

Different Adaption Strategies of Abundant and Rare Microbial Communities in Sediment and Water of East Dongting Lake.

The dynamics of aquatic microbes is of great importance for comprehending the acclimatisation and evolution of microorganisms in lake ecology. However, little is known about the adaption strategies of microbial communities in East Dongting Lake, which had special and complexity geographical characteristics. A semi-enclosed lake area (A) and a waterway connected to Yangtze River (B) both existed in the lake zone. Here, we investigated bacterial and fungal community diversity, community network and community assembly processes in sediment and water. The results indicated that the proportion of OTU numbers and their relative abundance for rare and abundant taxa were different obviously between sediment and water, but not between bacteria and fungi. However, abundant subcommunities dominated the shifts of bacterial community diversity and structure in A region, while rare subcommunities for fungal community diversity. Compared to fungal community, bacterial network was more compact and more key stones were identified as rare taxa. In addition, stochastic processes (dispersal limitation) drove the community assembly of abundant and rare subcommunities, but the effects of deterministic processes (including variable and heterogeneous selections) affected more on rare rather than abundant taxa. Partial Mantel test further indicated that the effect of environmental factors was a stronger force in shaping abundant bacterial subcommunities (TOC, NH4+-N, TN, and ORP) and rare fungal subcommunities (ORP). Environmental factors explained more of the variation in bacterial community structure than that in fungal community structure, although they had additional effects on fungal community diversity and community assembly. Moreover, bacterial community affected the fungal community as a biotic factor in water. This research provided new insights into better understanding of microbial communities in the complex environment of the East Dongting Lake.

Biotic and abiotic properties mediating sediment microbial diversity and function in a river–lake continuum

A river–lake system plays an important role in water management by providing long-term and frequent water diversions. However, hydrological connectivity in the system can have a profound effect on sediment microbial communities through pH, nutrient concentrations, and benthos invertebrates. Consequently, identifying the key environmental factors and their driving mechanisms is vital for microbial adaptation strategies to extreme environments. In this study, we analyzed the significant difference in sediment bacterial and fungal community structures and diversity indices among Dongting Lake and its tributary rivers, which worked as a typical river-connected lake ecosystem. There were significant differences in biotic and abiotic environments in the sediment habitats of Dongting Lake and its tributary rivers. Random forest analysis revealed that pH and Mollusca were found to be the most important abiotic and biotic variables for predicting both bacterial and fungal community structures, respectively. The beta diversity decomposition analyses showed that the bacterial and fungal community compositional dissimilarities among different sections were dominated by species replacement processes, with more than half of the OTUs in each section being unique. Notably, both biotic and abiotic factors affected the number and the relative abundance of these bacterial and fungal unique OTUs, leading to changes in community composition. Mollusca, pH, TP, NO3-N, and NH4-N were negatively related to the relative abundance of Actinobacteria, Acidobacteria, Gemmatimonadetes, Planctomycetes, and Ascomycota, while Annelida and ORP were positively related to the relative abundance of Actinobacteria and Gemmatimonadetes. Additionally, PICRUSt analysis revealed that the functional dissimilarity among lakes and rivers was strengthened in unique species compared to all species in bacterial and fungal communities, and the changes of functional types helped to improve the habitat environment in the main Dongting Lake and promote the process of microbial growth. From our results, the role of macrozoobenthos and physicochemical characteristics in driving the sediment microbial community spatial variations became clear, which contributed to further understanding of the river–lake ecosystem.

Winter Grazing, Not Fencing or Unicast, Promotes Stability of Microbial Community and Function in the Qilian Mountains of Qinghai‐Xizang Plateau

ABSTRACTIn alpine meadows, microorganisms are essential to sustain the stability of terrestrial geochemical processes and vegetation–soil–microbial systems. The present study in order investigate how various management measures impact the microbial communities' composition and functionality, we utilize metagenomic sequencing techniques to examinate the composition and function of soil microbial communities in the southern Qilian Mountains of the Qinghai‐Xizang Plateau in response to the management practices of fencing enclose (FE), winter grazing (WG), transition zone between natural and artificial grasslands (TZ), and artificial unicast oats (AU). Vegetation diversity and soil physicochemical characteristics were dramatically altered by the management measures. The prokaryotic community structure was considerably similar in FE and WG, as well as in TZ and AU. Near‐natural (FE) and artificial establishment (AU) disturbances changed the fungal community structure. Enzymes related to carbon metabolism did not respond significantly to the management measures, whereas those related to nitrogen metabolism did not respond significantly in TZ and AU. The relative abundance of enzymes participating in nitrogen metabolism was higher under TZ and AU than under FE and WG. We concluded that grassland management measures altered the structure of aboveground graminoid and leguminous vegetation communities and belowground biomass allocation, resulting in changes in K uptake, causing striking changes in the structure of fungal communities and nitrogen‐metabolizing enzymes; moderate disturbance (WG) was beneficial for maintaining the stability of microbial communities in alpine grasslands.

Effects of the Radicle Sheath on the Rhizosphere Microbial Community Structure of Seedlings in Early Spring Desert Species Leontice incerta

Most research on plant–microbe interactions emphasize the effects of micronutrients on the rhizosphere microbial community structure. However, the influence of seed structures, particularly the radicle sheath, on microbial diversity at the seedling root tips under varying temperatures and humidity has been less explored. This study conducted controlled indoor experiments in the northern desert of Xinjiang to assess the radicle sheath’s impact on microbial community composition, diversity, and function. The results indicated no significant changes in the Chao1 index for bacteria and fungi, but notable differences were observed in the Shannon and Simpson indices (p < 0.05). Under drought conditions, the radicle sheath significantly reduced bacterial infections without affecting fungi. Genus-level analysis showed an increased abundance of specific dominant bacterial groups when the radicle sheath was retained. NMDS analysis confirmed its significant effect on both bacterial and fungal community structures. LEfSe analysis identified 34 bacterial and 15 fungal biomarkers, highlighting the treatment’s impacts on microbial taxonomic composition. Functional predictions using PICRUSt 2 revealed that the radicle sheath facilitated the conversion of CH4 to CH3OH and various nitrogen cycle processes under drought. Overall, the radicle sheath plays a crucial role in maintaining rhizosphere microbial community stability and enhancing the functions of both bacteria and fungi under drought conditions.

Altitude Distribution Patterns and Driving Factors of Rhizosphere Soil Microbial Diversity in the Mountainous and Hilly Region of Southwest, China

The distribution characteristics of the microbial community in rhizosphere soils of different altitudinal gradients were explored to uncover ecological factors affecting microbial community composition. In this study, the community variations of bacteria and fungi in the rhizosphere soil of Chrysanthemum indicum L. were analyzed. Samples were distributed along an altitudinal gradient of 300–1500 m above sea level in the Fuling watershed of the Three Gorges Reservoir area, China. The analysis was conducted using Illumina MiSeq high-throughput sequencing and bioinformatics analyses. Through correlation analysis with ecological factors, the altitude distribution pattern and driving factors of soil microbial diversity in the mountainous and hilly region of Chongqing were explored. According to the results, the richness and diversity of rhizosphere soil bacteria increased with altitude, while fungi were the richest and most diverse at an altitude of 900 m. The composition of the microbial community differed among different altitudes. Actinobacteria, Proteobacteria, Acidobacteriota, Chloroflexi, Bacteroidota, Ascomycota, unclassified_k_Fungi, Basidiomycota, and Mortierellomycota dominated the microbial community in rhizosphere soil. Correlation analysis showed that the distribution of rhizosphere soil microbial communities correlated with soil ecological factors at different altitudes. Moisture, pH, total nitrogen, total potassium, available potassium, urease, and catalase were significantly positively correlated with rhizosphere soil bacterial α-diversity, while their correlations with fungi were not significant. Variation partition analysis showed that the combined effects of soil physical and chemical factors, enzyme activity, and microbial quantity regulated bacterial community structure and composition. Their combined contributions (19.21%) were lower than the individual effects of soil physical and chemical factors (48.49%), enzyme activity (53.24%), and microbial quantity (60.38%). The effects of ecological factors on fungal communities differed: While the soil physical and chemical factors (44.43%) alone had a clear effect on fungal community structures, their combined contributions had no apparent effect. The results of this study not only contribute to a deeper understanding of the impact mechanism of altitude gradient on the diversity of rhizosphere soil microbial communities, but also provide a scientific basis for the protection and management of mountainous and hilly ecosystems. It lays a foundation for the future exploration of the relationship between microbial communities and plant–soil interactions.

Fungal community characteristics of the last remaining habitat of three paphiopedilum species in China.

Paphiopedilum armeniacum, Paphiopedilum wenshanense and Paphiopedilum emersonii are critically endangered wild orchids. Their populations are under severe threat, with a dramatic decline in the number of their natural distribution sites. Ex situ conservation and artificial breeding are the keys to maintaining the population to ensure the success of ex situ conservation and field return in the future. The habitat characteristics and soil nutrient information of the last remaining wild distribution sites of the three species were studied. ITS high-throughput sequencing was used to reveal the composition and structure of the soil fungal community, analyze its diversity and functional characteristics, and reveal its relationship with soil nutrients. The three species preferred to grow on low-lying, ventilated and shaded declivities with good water drainage. There were significant differences in soil alkali-hydrolyzed nitrogen and available phosphorus among the three species. There were 336 fungal species detected in the samples. On average, there were different dominant groups in the soil fungal communities of the three species. The functional groups of soil fungi within their habitats were dominated by saprophytic fungi and ectomycorrhizae, with significant differences in diversity and structure. The co-occurrence network of habitat soil fungi was mainly positive. Soil pH significantly affected soil fungal diversity within their habitats of the three paphiopedilum species. The study confirmed that the dominant groups of soil fungi were significantly correlated with soil nutrients. The three species exhibit comparable habitat inclinations, yet they display substantial variations in the composition, structure, and diversity of soil fungi. The fungal functional group is characterized by a rich presence of saprophytic fungi, a proliferation of ectomycorrhizae, and a modest occurrence of orchid mycorrhizae. The symbiotic interactions among the soil fungi associated with these three species are well-coordinated, enhancing their resilience against challenging environmental conditions. There is a significant correlation between soil environmental factors and the composition of soil fungal communities, with pH emerging as a pivotal factor regulating fungal diversity. Our research into the habitat traits and soil fungal ecosystems of the three wild Paphiopedilum species has established a cornerstone for prospective ex situ conservation measures and the eventual reestablishment of these species in their native landscapes.

Microbial community composition and co-occurrence network analysis of the rhizosphere soil of the main constructive tree species in Helan Mountain of Northwest China

To understand the microbial diversity and community composition within the main constructive tree species, Picea crassifolia, Betula platyphylla, and Pinus tabuliformis, in Helan Mountain and their response to changes in soil physicochemical factors, a high throughput sequencing technology was used to analyze the bacterial and fungal diversity and community structure. RDA (Redundancy Analysis) and Pearson correlation analysis were used to explore the influence of soil physicochemical factors on microbial community construction, and co-occurrence network analysis was conducted on the microbial communities. The results showed that the fungal and bacterial diversity was highest in B. platyphylla, and lowest in P. crassifolia. Additionally, the fungal/bacterial richness was greatest in the rhizosphere soils of P. tabuliformis and B. platyphylla. RDA and Pearson correlation analysis revealed that NN (nitrate nitrogen) and AP (available phosphorus) were the main determining factors of the bacterial community, while NN and SOC (soil water content) were the main determining factors of the fungal community. Pearson correlation analysis between soil physicochemical factors and the alpha diversity of the microbial communities revealed a significant positive correlation between pH and the bacterial and fungal diversity, while SOC, TN (total nitrogen), AP, and AN (available nitrogen) were significantly negatively correlated with the bacterial and fungal diversity. Co-occurrence network analysis revealed that the soil bacterial communities exhibit richer network nodes, edges, greater diversity, and greater network connectivity. Indicating that bacterial communities exhibit more complex and stable interaction patterns in soil. This study reveals the complex interactive relationship between microbial communities and soil physicochemical factors in forest ecosystems. By analyzing the response of rhizosphere microbial communities of major tree species in Helan Mountain to nutrient dynamics and pH changes, we can deepen our understanding of the role of microorganisms in regulating ecosystem functions and provide theoretical basis for soil improvement and ecological restoration strategies.

The Fungal Side of the Story: Saprotrophic- vs. Symbiotrophic-Predicted Ecological Roles of Fungal Communities in Two Meromictic Hypersaline Lakes from Romania

Over three-quarters of Earth’s surface exhibits extreme environments where life thrives under harsh physicochemical conditions. While prokaryotes have often been investigated in these environments, only recent studies have revealed the remarkable adaptability of eukaryotes, in particular fungi. This study explored the mycobiota of two meromictic hypersaline lakes, Ursu and Fără Fund, in Transylvania (Romania). The intrinsic and extrinsic fungal diversity was assessed using amplicon sequencing of environmental DNA samples from sediments, water columns, surrounding soils, and an associated rivulet. The fungal communities, illustrated by the 18S rRNA gene and ITS2 region, exhibited contrasting patterns between the lakes. The ITS2 region assessed better than the 18S rRNA gene the fungal diversity. The ITS2 data showed that Ascomycota was the most abundant fungal group identified in both lakes, followed by Aphelidiomycota, Chytridiomycota, and Basidiomycota. Despite similar α-diversity levels, significant differences in fungal community structure were observed between the lakes, correlated with salinity, total organic carbon, total nitrogen, and ammonium. Taxonomic profiling revealed depth-specific variations, with Saccharomycetes prevalent in Ursu Lake’s deeper layers and Lecanoromycetes prevalent in the Fără Fund Lake. The functional annotation using FungalTraits revealed diverse ecological roles within the fungal communities. Lichenized fungi were dominant in Fără Fund Lake, while saprotrophs were abundant in Ursu Lake. Additionally, wood and soil saprotrophs, along with plant pathogens, were more prevalent in the surrounding soils, rivulet, and surface water layers. A global overview of the trophic relations in each studied niche was impossible to establish due to the unconnected graphs corresponding to the trophic interactions of the analyzed fungi. Plotting the unweighted connected subgraphs at the genus level suggests that salinity made the studied niches similar for the identified taxa. This study shed light on the understudied fungal diversity, distribution, and ecological functions in hypersaline environments.

Rhizosphere microbial community structure in the water-level-fluctuation zone under distinct waterlogging stresses

Rhizosphere microbial communities are believed to be vital in the adaption of dominant plants to strong waterlogging stress in the water-level-fluctuation zone (WLFZ). However, limited knowledge is available on their patterns in the WLFZ under distinct waterlogging stresses. Here, rhizosphere and non-rhizosphere bacterial and fungal communities derived from two typical dominant plants (Rumex acetosa L. and Oxybasis glauca) in the WLFZ of Three Gorges Reservoir, China were analysed through high-throughput sequencing. A total of 63 phyla, 173 classes, 259 orders, 287 families and 518 genera of bacteria, as well as 15 phyla, 50 classes, 124 orders, 265 families and 652 genera of fungi were detected in soils with different waterlogging stress intensities. The most dominant bacterial and fungal phyla in each sample are Proteobacteria and Ascomycota, respectively. Bacteria and fungi in soil may increase their microbial ɑ diversity under the intensity of waterlogging stress to cope with this stress. LEfSe analysis showed that the impact of waterlogging stress on fungal community structure in soil is more prominent than that on bacteria. Key fungal biomarkers can be found in each soil sample, but in many samples, key bacterial biomarkers cannot be found. The metabolic pathways related to aerobic respiration type I and de novo biosynthesis of adenosine ribonucleotides dominate in the microbial community. Redundancy analysis revealed that the structure of rhizosphere microbial communities in different plants is significantly influenced by environmental factors. This study provides a theoretical basis for understanding the relationship between plants and their second genome (rhizosphere microorganisms) in extreme habitats, such as the WLFZ of large reservoirs.

Prescribed burning alters soil microbial community structure by changing soil physicochemical properties in temperate forests of northern China

Prescribed burning is commonly used to maintain forest ecosystem functions and reduce the risk of future wildfires. Although many studies have investigated the response of microbial community to wildfires in forest ecosystems, the effects of prescribed burnings on soil microbial community structure are less studied. It is also unclear that how post-fire soil physiochemical properties changes affected soil microbial communities. Here, we studied the impacts of prescribed burning on soil microbiome in three typical temperate forests of northern China by collecting soil physicochemical and high-throughput sequencing for 16S rRNA and 18S rRNA was applied to analyze the diversity and community composition of soil microbes (bacteria and fungi). Compared with pre-fire condition, prescribed burning significantly decreased Chao1 index and altered soil bacterial communities (P < 0.05), whereas it had no significant effect on fungal diversity and community structure of the (P > 0.05). Planctomycetes and Actinobacteria made the greatest contributions to the bacterial community dissimilarity between the pre-fire and post-fire conditions. The main variables influencing the post-fire soil microbial community structure are soil pH, available phosphorus, total nitrogen, and the ratio of soil total carbon to soil total nitrogen, which could account for 73.5% of the variation in the microbial community structure in these stands. Our findings demonstrated a great discrepancy in the responses of bacteria and fungi to prescribed burning. Prescribed burning altered the soil microbial structure by modifying the physicochemical properties. Our results pointed that it is essential to evaluate the impact of prescribed burnings on forest ecosystem functions. These findings provide an important baseline for assessing post-fire microbial recovery in the region and offer critical guidance for restoration efforts.

Comparative analysis of crop rotation systems: the impact of ginger (Zingiber officinale) and sponge gourd (Luffa aegyptiaca) residues on growth of Chinese cabbage (Brassica rapa var. chinensis).

Continuous cropping in greenhouse cultivation often leads to increased pest and disease problems, reducing crop quality and yield. Crop rotation is a common strategy to address these issues. This study compared the growth of Chinese cabbage (Brassica rapa var. chinensis) following rotations with ginger (Zingiber officinale) and sponge gourd (Luffa aegyptiaca). The Chinese cabbage exhibited normal growth following ginger rotation but showed abnormal growth after sponge gourd rotation. The study investigated the underlying causes by analyzing soil physicochemical properties and rhizosphere microbial communities of Chinese cabbage using 16S rRNA and ITS sequencing. The results revealed that soil from ginger-Chinese cabbage rotation had higher levels of soil organic carbon (SOC) and available phosphorus (AP), but lower total nitrogen (TN) and available potassium (AK). Despite similar alpha-diversity for both bacterial and fungal communities, distinct bacterial and fungal community structures between two rotation cropping systems were observed. This suggests that even if the alpha-diversity does not change, the composition of the microbial community can shift in ways that might influence soil health and plant growth. Furthermore, redundancy analysis revealed a significant correlation between microbial community structures and soil physicochemical properties of two rotation cropping systems. The SOC and TN were revealed to be the most significant of the investigated soil physicochemical parameters with respect to the variation of both bacterial and fungal assemblages, respectively. The identified biomarkers in bacterial community composition further emphasize the potential for specific microbes to influence crop health positively or negatively. We found that the indicator genera of the bacterial community composition of the ginger-Chinese cabbage rotation system were Amycolatopsis (genus), Pseudonocardiales (order), Pseudonocardiaceae (family), and Amycolatopsis mediterranei, which are known as producers of secondary metabolites, such as antibiotics. These findings highlight the importance of crop selection in rotation strategies for optimizing agricultural outcomes.

Trichoderma Rhizosphere Soil Improvement: Regulation of Nitrogen Fertilizer in Saline–Alkali Soil in Semi-Arid Region and Its Effect on the Microbial Community Structure of Maize Roots

In order to reduce the actual impact of a saline–alkali environment on maize production in semi-arid areas, it is particularly important to use the combined fertilization strategy of Trichoderma microbial fertilizer and nitrogen fertilizer. The purpose of this study was to investigate the effects of different concentrations of nitrogen fertilizer combined with Trichoderma on improving the structural characteristics and ecological functions of maize rhizosphere microbial community in semi-arid saline–alkali soil. Through the microbiome analysis of maize rhizosphere soil samples with 60 kg N·ha−1 (N1) and 300 kg N·ha−1 (N2) nitrogen fertilizer combined with Trichoderma (T1) and without Trichoderma (T0), we found that the combination of Trichoderma and different concentrations of nitrogen fertilizer significantly affected the structure of bacterial and fungal communities. The results of this study showed that the combination of Trichoderma and low-concentration nitrogen fertilizer (N1T1) could improve soil nutritional status and enhance its productivity potential, revealing the relationship between beneficial and harmful fungal genera, microbial diversity and abundance, and crop biomass, which is of great significance for improving agricultural production efficiency and sustainable development.

Phyllosphere of Agathis australis Leaves and the Impact of the Soil-Borne Pathogen Phytophthora agathidicida

Leaf surface microbial communities play an important role in forest ecosystems and are known to be affected by environmental and host conditions, including diseases impacting the host. Phytophthora agathidicida is a soil-borne pathogen that causes severe disease (kauri dieback) in one of New Zealand’s endemic trees, Agathis australis (kauri). This research characterised the microbial communities of the A. australis phyllosphere (i.e. leaf surface) using modern molecular techniques and explored the effects of P. agathidicida on those communities. Fresh leaves were collected from trees where P. agathidicida was and was not detected in the soil and characterisation of the leaf surface microbial community was carried out via high-throughput amplicon sequencing of the internal transcribed spacer (ITS) and 16S ribosomal RNA regions. Nutrients in leaf leachates were also measured to identify other possible drivers of microbial diversity. The dominant phyllosphere microbial phylum was Proteobacteria followed by Acidobacteria. The phyllosphere microbial richness of A. agathis associated with P. agathidicida-infected soils was found to be generally lower than where the pathogen was not detected for both prokaryote (bacterial) and fungal phyla. Leaf leachate pH as well as boron and silicon had significant associations with bacterial and fungal community structure. These findings contribute to the development of a comprehensive understanding of A. australis leaf surface microbial communities and the effects of the soil pathogen P. agathidicida on those communities.

Decoupled fungal and bacterial functional responses to biochar amendment drive rhizosphere priming effect on soil organic carbon mineralization

The application of biochar to soil is widely recognized as a promising strategy for enhancing the accumulation and stability of soil organic carbon (SOC), which is crucial in mitigating climate change. However, the influence of interactions between plants and biochar on soil microbial communities and their involvement in SOC mineralization and stability remains unclear. This understanding is essential for optimizing carbon (C) sequestration in systems involving plants, soil, and biochar. In this study, employing a 13C natural abundance approach, we investigated the effect of biochar on the maize rhizosphere priming effect (RPE) in paddy soil. We also examined alterations in microbial communities and functional genes related to C degradation and fixation. Over the 99 days of maize growth, biochar application increased RPE and total SOC while decreasing dissolved organic C. It also elevated soil pH, resulting in shifts in fungal and bacterial community structure, favoring oligotrophic species. Fungal and bacterial assemblies were dominated by deterministic and stochastic processes, respectively. While the abundance of fungal guilds varied irregularly, bacterial guilds were uniformly enriched under biochar-plant interactions. Functional traits such as ecoenzymatic activities, bacterial guilds, and functional genes predominantly affected RPE under biochar application. Bacterial functional genes associated with C degradation and fixation were concurrently enhanced with biochar application. Our results indicate that interactions between plants and biochar can enhance native SOC mineralization and accumulation in a short timeframe by modulating functional traits of soil microorganisms, particularly the bacterial community involved in C degradation and fixation.Graphical

Diversity and Functional Characteristics of Fungal Communities and Influencing Factors in Typical Paddy Fields of China

To investigate the structure, diversity, and function of different paddy soil fungal communities and the factors affecting them in typical paddy cropping areas in China, five typical Chinese paddy soils were selected in this study, and the composition and diversity of soil fungal communities were comparatively analyzed using high-throughput sequencing technology and functionally predicted using the FUNGuild microecological tool. The results showed that： ① The fungal community diversity of soil samples from Heilongjiang （HLJ） was significantly lower than that of the other four regions （P<0.05）； the highest fungal community richness was found in paddy soils from Yunnan （YN）, which was significantly higher than that of the other regions （P<0.05）； and the soil samples from Hainan （HN）, Jiangxi （JX）, and Shandong （SD） were relatively close to each other. The highest average relative abundance at the level of the five typical paddy phyla was Ascomycota, and the genus with the highest average relative abundance was Tausonia. ② Fungi had the largest proportion of saprophytic trophic types, and their corresponding environmental functions were stronger. ③ The species abundance of soil fungi was highly significantly correlated with soil TP, EC, and BD （P<0.01）, and redundancy analyses also showed that soil TP was the main driver of the fungal community as well as the saprophytic functional taxa. The above results showed that the soil fungal community diversity and structure varied greatly among samples, and the relative abundance of fungal genera was affected by soil physical and chemical properties and altered the fungal community structure in paddy fields. The development of this study will provide theoretical references for the sustainable management based on fungal diversity and function of paddy fields.