Seasonal variations of soil fungal diversity and communities in subalpine coniferous and broadleaved forests

Decoding endosperm endophytes in Pinus armandi: a crucial indicator for host response to climate change

BACKGROUND

Plant-associated microorganisms significantly contribute to plant survival in diverse environments. However, limited information is available regarding the involvement of endophytes in responding to climate change and their potential to enhance host plants' adaptation to future environmental shifts. Pinus armandi, endemic to China and widely distributed in climate-sensitive regions, serves as an ideal subject for investigating microbiome interactions that assist host plants in climate change response. Despite this, a comprehensive understanding of the diversity, community composition, and factors influencing endosperm endophytes in P. armandi, as well as the response of these endophytes to climate change, remains elusive.

RESULTS

In this study, transcriptome data from 55 P. armandi samples from 13 populations were analyzed to evaluate the composition and diversity of active endosperm endophytes and predict their response to future climate change. The results revealed variations in community composition, phylogenetic diversity, and interaction network between the northern and southern groups. Temperature and precipitation correlated with endosperm endophytic species richness and diversity. Under projected future climate conditions, the northern group exhibits greater genomic vulnerability and anticipates increased threats, reflecting a corresponding trend in endosperm endophytes, particularly within the Ascomycota community.

CONCLUSION

The consistent threat trend from climate change impacting both hosts and endophytes emphasizes the potential importance of host-related fungi as crucial indicators for predicting future climate impacts. Meanwhile, this study establishes an initial framework for exploring host-microbial interactions within the context of climate warming and provides valuable insights for studies related to plant protection.

Diversity of Endophytic Fungi in Plant Species: Traditional vs. High-Throughput Sequencing Approaches

The plant microbiome significantly impacts plant life, with fungi playing a crucial role in shaping interactions and classifications. Advances in cultivation technologies have refined fungal classification, and research highlights the vital connection between endophytic fungi and their plant hosts. The present study employs morphological and phylogenetic techniques, predicting the Internal Transcribed Spacer 2 (ITS2) secondary structure and using next-generation sequencing (NGS) data to detect fungal endophytes in plant leaves via both traditional and conventional approaches. The research area, with its hot semi-arid environment and red and black soils, supports drought-resistant plants like Senna auriculata, Ziziphus mauritiana, and Catunaregam spinosa, known for their medicinal properties. These plants, rich in antioxidants, play a vital role in traditional medicine and highlight the region's rich ethno-botanical heritage. The culture-dependent study on the foliage yielded a total of 17 isolates from S. auriculata and 16 each from both C. spinosa and Z. mauritiana. The most common genera, Alternaria and Nigrospora, account for 18.3% of all isolated endophytic fungi. Three plants were colonized with Nigrospora and Lasiodiplodia, and their morphotypes were determined using ITS2 secondary structure prediction. Recent ecological studies highlight unculturable taxa, or dark taxa, where many species cannot sporulate or be cultured, emphasizing the need for High - Throughput Sequencing (HTS) approaches. The study gathered 68,791 reads from S. auriculata with 101 operational taxonomic units (OTUs), 58,620 from C. spinosa with 219 OTUs, and 66,087 from Z. mauritiana with 193 OTUs, with the majority of OTUs related to Colletotrichum (69%) and a minimum of Myrmaecium (2%). A total of 49 fungal isolates were obtained from traditional methods, whereas 513 fungal OTUs were retrieved through HTS methods, confirming the presence of a highly abundant fungus population in plant samples. The study reveals that using the ITS short amplicon sequencing technique provides distinct insights into endophytic fungal communities in three plant samples. In conclusion, analyzing plant fungal components using a combination of culture-dependent and culture-independent techniques may be a novel strategy.

Effects of fertilization on litter decomposition dynamics and nutrient release in orchard systems

Plant litter decomposition is a significant ecosystem function that regulates nutrient cycling, soil fertility, and biomass production. It is heavily regulated by nutrient intake. The effects of exogenous nutrients on litter decomposition are not yet fully understood. To determine how Eriobotrya japonica litter decomposition responds to adding nutrients, we used the decomposition litter bag method in the laboratory for 180 days. There were five different nutrient treatment levels were used: control (no addition), low nitrogen addition (LN; 100 kg N·ha-1·year-1), high nitrogen addition (HN; 200 kg N·ha-1·year-1), phosphorus addition (P; 50 kg P·ha-1·year-1), and micronutrient addition (M; 50 kg M·ha-1·year-1). According to a repeated-measures analysis of variance, adding N reduced the remaining mass (p < 0.01) by 4.1% compared to the CK group. In contrast, adding M increased the remaining mass (p < 0.01) by 6.8% compared to the CK group. Adding P had no significant effect on the remaining mass. Although the amount of residual carbon (C) was unaffected, adding N increased the level of residual N in the litter. Litter C content, K content, N concentration, and C/N ratio were linearly correlated to the remaining litter (p < 0.01). Although adding nutrients decreased soil enzyme activity later in the decomposition process, no significant correlation was detected between enzyme activity and the remaining mass. N fertilization treatments decreased the soil microbial diversity index. The addition of nitrogen and micronutrients reduced the abundance of Acidobacteria, while HN addition increased the abundance of Actinobacteria. The addition of micronutrients increased the abundance of Proteobacteria. These results imply that N-induced alterations in the element content of the litter regulated the effects of nutrient inputs on litter decomposition. This study can be a reference for the fertilization-induced decomposition of agricultural waste litter.

Extramatrical mycelial biomass is mediated by fine root mass and ectomycorrhizal fungal community composition across tree species

In many ecosystems, a large fraction of gross primary production is invested in mycorrhiza. Ectomycorrhizal (ECM) mycelium is involved in regulating soil carbon and nutrient cycling. However, little is known about how mycelial biomass, production and turnover differ depending on ECM fungal community composition and associated tree species. We quantified fine root biomass and length using soil cores, and mycelial traits (biomass, production, and turnover) using mesh-bags and ergosterol analysis, and identified ECM exploration types by Illumina MiSeq sequencing of four ECM-dominated tree species (Picea asperata, Larix gmelinii, Quercus aquifolioides and Betula albosinensis) in subalpine forest. The ECM fungal community composition separated between needle-leaved and broadleaved species, and between evergreen and deciduous species. The ratio of mycelial to fine root biomass was similar across the species regardless of genus-scale community composition and the relative abundance of exploration types. Compared to the other species, Q. aquifolioides displayed higher fine root biomass and mycelial biomass and production, dominated by contact-short exploration type. Mycelial turnover rate tended to be lowest in P. asperata, dominated by medium-long exploration type. Much higher production of mycelium and only slightly higher turnover rate in Q. aquifolioides suggests that its steady-state mycelial biomass would be higher than of the other species. Moreover, compared to the two deciduous species, with similar production but somewhat lower turnover rate, the standing crop of mycelium in P. asperata may stabilize at a higher value. Our findings, that exploration type may affect production and turnover, highlight the importance of characterizing ECM fungal communities by exploration types when estimating the contribution of mycelium biomass to forest carbon sink and storage.

Soil Fungal Community Diversity, Co-Occurrence Networks, and Assembly Processes under Diverse Forest Ecosystems

Fungal communities are critical players in the biogeochemical soil processes of forest ecosystems. However, the factors driving their diversity and community assembly are still unclear. In the present study, five typical vegetation types of soil fungal communities in Liziping Nature Reserve, China, were investigated using fungal ITS sequences. The results show that the topsoil fungal community is mainly dominated by the phyla Ascomycota, Basidiomycota, and Mortierellomycota. Although there was no significant difference in α diversity (Shannon, Simpson, and Pielou evenness indices) among different forest types, there was a significant difference in β diversity (community composition). This study found that soil pH, soil organic carbon, total nitrogen (TN), total phosphorus (TP), and the total nitrogen/total phosphorus (N/P) ratio are the main environmental factors that affect soil fungal communities. Each forest type has a specific co-occurrence network, indicating that these community structures have significant specificities and complexities. Deciduous evergreen broad-leaved forests as well as deciduous broad-leaved and evergreen broad-leaved mixed forests showed high modularity and average path lengths, indicating their highly modular nature without distinct small-scale characteristics. Furthermore, our findings indicate that the structures of topsoil fungal communities are mainly shaped by stochastic processes, with the diffusion limitation mechanism playing a particularly significant role.

Biogeographic and co-occurrence network differentiation of fungal communities in warm-temperate montane soils

Studying the biogeographic patterns of fungal communities across altitudinal and soil depth gradients is essential for understanding how environmental variations shape the diversity and functionality of these complex ecological assemblages. Here, we evaluated the response and assembly patterns of fungal communities to altitude and soil depth, and the co-occurrence patterns influencing soil fungal metabolic preferences on Dongling Mountain. We observed significant variations in fungal β-diversity, driven by elevation and soil depth, with climatic parameters (MAT and MAP) and nutrient concentrations (TOC, TP, and TN) serving as prominent influencers. Additionally, we found that the multiple substrate-induced respiration rate of fungi degrading various carbon substrates was diminished in high-altitude and subsurface soils compared to low-altitude and surface soils. Stochastic processes play a more important role in controlling fungal community assembly than deterministic processes, with dispersal limitation emerging as the main driver of community assembly. While greater network complexity was evident in the topsoil compared to the subsoil, both layers harbored altitude-sensitive OTUs (asOTUs) that belonging to distinct modules. Moreover, fungal groups sensitive to the same altitude exhibited similar metabolic preferences. The asOTUs designated for lower altitude areas favored unstable carbon substrates (glucose and sucrose), while those designated as higher altitude areas exhibited a preference for recalcitrant carbon (xylan and lignin). This evidence suggests that soil fungal communities respond to environmental changes by trading off their life strategies and metabolic characteristics.

Spatial variations impact the soil fungal communities of Larix gmelinii forests in Northeast China

Soil fungi play a critical role in the biogeochemical cycles of forest ecosystems. Larix gmelinii is a strong and important timber tree species, which forms close associations with a wide range of soil fungi. However, the temporal-spatial disparity effects on the assembly of soil fungal communities in L. gmelinii forests are poorly understood. To address these questions, a total of 120 samples, including 60 bulk soil and 60 root samples, were collected from Aershan and Genhe in July (summer) and October (autumn)2021. We obtained 7,788 operational taxonomic units (OTUs) after merging, filtering, and rarefying using high-throughput sequencing. The dominant phyla are Basidiomycota, Ascomycota, Mortierellomycota, and Mucoromycota. There were 13 dominant families, among which the families with average relative abundance more than 5% included Thelephoraceae, Mortierellaceae, Archaeorhizomycoaceae, and Inocybaceae. In the functional guilds, symbiotrophic fungi had a relative advantage in the identified functions, and the relative abundances of pathotrophic and saprotrophic fungi varied significantly between sites. There were 12 families differentially expressed across compartments, 10 families differentially expressed between seasons, and 69 families were differentially expressed between sites. The variation in alpha diversity in the bulk soil was greater than that in the rhizosphere soil. Among the three parts (compartment, season, and site), the site had a crucial effect on the beta diversity of the fungal community. Deterministic processes dominated fungal community assembly in Genhe, whereas stochastic processes dominated in Aershan. Soil physicochemical properties and climatic factors significantly affected fungal community structure, among which soil total nitrogen and pH had the greatest effect. This study highlights that spatial variations play a vital role in the structure and assembly of soil fungal communities in L. gmelinii forests, which is of great significance for us in maintaining the health of the forests.

Metal-immobilizing Pseudomonas taiwanensis WRS8 reduces heavy metal accumulation in Coriandrum sativum by changing the metal immobilization-related bacterial population abundances

Metal-immobilizing bacteria play a critical role in metal accumulation in vegetables. However, little is known concerning the mechanisms involved in bacteria-induced reduced metal availability and uptake in vegetables. In this study, the impacts of metal-immobilizing Pseudomonas taiwanensis WRS8 on the plant biomass, Cd and Pb availability and uptake in two coriander (Coriandrum sativum L.) cultivars, and bacterial community structure were investigated in the polluted soil. Strain WRS8 increased the biomass of two coriander cultivars by 25-48% and reduced Cd and Pb contents in the edible tissues by 40-59% and available Cd and Pb contents in the rhizosphere soils by 11.1-15.2%, compared with the controls. Strain WRS8 significantly increased the pH values and relative abundances of the dominant populations of Sphingomonas, Pseudomonas, Gaiellales, Streptomyces, Frankiales, Bradyrhizobium, and Luteimonas, while strain WRS8 significantly decreased the relative abundances of the dominant populations of Gemmatimonadaceae, Nitrospira, Haliangium, Paenibacillus, Massilia, Bryobacter, and Rokubacteriales and the rare bacterial populations of Enterorhabdus, Roseburia, Luteibacter, and Planifilum in the rhizosphere soils, compared with the controls. Significantly negative correlations were observed between the available metal concentrations and the abundances of Pseudomonas, Luteimonas, Frankiales, and Planifilum. These results implied that strain WRS8 could affect the abundances of the dominant and rare bacterial populations involved in metal immobilization, resulting in increased pH values and decreased metal availability and uptake in the vegetables in the contaminated soil.

The impact of novel azotobacter Bacillus sp. T28 combined sea buckthorn pomace on microbial community structure in paddy soil

Nitrogen (N) fertilizer application is an essential part of agricultural production in order to improve rice yields. However, long-term irrational application and low utilization of N fertilizer have caused a series of environmental problems. Biofertilizer is considered an effective alternative to N fertilizer. In this study, the effect of biofertilizer made of diazotrophic bacteria Bacillus sp. T28 combined with sea buckthorn pomace on the soil N changes and microbial community structure was conducted. Compared to CK, NO₃^--N content decreased 33.1%-43.8% and the rate of N₂O release decreased 8-26 times under different fertilizer treatments during incubation of 0-7 days. On the contrary, NH₄⁺-N in T28 with or without sea buckthorn pomace treatments increased by 56.5-118.8% during incubation of 7-14 days. The results indicated that this biofertilizer reduced the environmental risk associated with the accumulation of NO₃^--N in paddy soil and the release of N₂O to the atmosphere and maintained the soil available N supply capacity. Besides, applying Bacillus T28 with sea buckthorn pomace increased the abundance of soil N functional genes such as nifH, narG, nirS, nirK, and nosZ. The ¹³C-PLFAs results demonstrated that this biofertilizer improves soil microbial community diversity, nutrient turnover rate and ecosystem stability by altering soil pH and total carbon (TC). In conclusion, Bacillus sp. T28 combined with sea buckthorn pomace regulated the indigenous soil microbial community structure and mitigated the environmental risk of conventional N fertilization in agroecosystems.

Soil properties and root traits are important factors driving rhizosphere soil bacterial and fungal community variations in alpine Rhododendron nitidulum shrub ecosystems along an altitudinal gradient

Both soil properties and plant root traits are pivotal factors affecting microbial communities. However, there is still limited information about their importance in shaping rhizosphere soil microbial communities, particularly in less-studied alpine shrub ecosystems. To investigate the effects of altitude (3300, 3600, 3900, and 4200 m) on the diversity and composition of rhizosphere soil bacterial and fungal communities, as well as the factors shaping rhizosphere soil microbial communities, we conducted this study in alpine Rhododendron nitidulum shrub ecosystems from the Zheduo mountain of the eastern Tibetan Plateau. Results demonstrated that bacterial community diversity and richness decreased to the lowest value at 3600 m and then increased at higher altitudes compared with 3300 m; whereas fungal richness at 3300 m was much lower than at other altitudes, and was closely related to soil properties and root traits. The composition of rhizosphere soil bacterial and fungal communities at the low altitude (3300 m) was different from that at high altitudes. Permutational multivariate analysis of variance and redundancy analysis indicated that soil properties (soil water content, pH, NO₃^--N, and available phosphorus) and root traits (surface area, and maximum depth) were the major factors explaining the variations of rhizosphere soil bacterial and fungal communities. Specific bacterial and fungal taxa along altitudes were identified. The bacterial taxa Planctomycetota was dominant at 3300 and 3600 m with low soil nutrient availability and high root surface area, whereas the fungal taxa Mortierellomycota was abundant at 3900 and 4200 m with high soil nutrient availability and low root surface area. These results suggested that different soil microbes can respond differently to altitude. This study provides a novel insight into factors driving rhizosphere soil bacterial and fungal community variations, which could improve our understanding of microbial ecology in alpine R. nitidulum shrub ecosystems along altitude.

Seasonal variation in the soil fungal community structure of Larix gmelinii forests in Northeast China

Soil fungi play an indispensable role in forest ecosystems by participating in energy flow, material circulation, and assisting plant growth and development. Larix gmelinii is the dominant tree species in the greater Khingan Mountains, which is the only cold temperate coniferous forest in China. Understanding the variations in underground fungi will help us master the situation of L. gmelinii above ground. We collected soil samples from three seasons and analyzed the differences in soil fungal community structure using high-throughput sequencing technology to study the seasonal changes in soil fungal community structure in L. gmelinii forests. We found that the Shannon and Chao1 diversity in autumn was significantly lower than in spring and summer. The community composition and functional guild varied significantly between seasons. Furthermore, we showed that ectomycorrhizal fungi dominated the functional guilds. The relative abundance of ectomycorrhizal fungi increased dramatically from summer to autumn and was significantly negatively correlated with temperature and precipitation. Temperature and precipitation positively affect the alpha diversity of fungi significantly. In addition, pH was negatively correlated with the Chao1 diversity. Temperature and precipitation significantly affected several dominant genera and functional guilds. Among the soil physicochemical properties, several dominant genera were affected by pH, and the remaining individual genera and functional guilds were significantly correlated with total nitrogen, available phosphorus, soil organic carbon, or cation exchange capacity. For the composition of total fungal community, temperature and precipitation, as well as soil physicochemical properties except AP, significantly drove the variation in community composition.

Distribution Pattern of Mangrove Fish Communities in China

Mangroves are among the most productive marine and coastal ecosystems and play an important role in maintaining the stability and diversity of fish communities. To explore the structure of mangrove fish communities in China, we compiled previous studies, monographs, and two databases on 54 mangrove areas published in the past 30 years. Mangrove fish communities in China comprised Osteichthys (597 species) and Chondrichthyes (14 species), representing 611 species in 344 genera, 117 families, and 28 orders. Perciformes were the predominant taxon, with 350 species in 52 families, accounting for 57% of the total species richness. Reef fish accounted for 29.62%. With regard to feeding groups, there were 328 carnivorous species (53.68%), 214 omnivorous species (35.02%), 41 herbivorous species (6.71%), and 28 detritivores species (4.58%). Classified by body size, 57.61% were small-sized, 24.22% medium-sized, and 18.17% were large-sized fishes. A total of 5.23% (32 species) of these mangrove fish are currently on IUCN red lists, i.e., 2 species are critically endangered, 4 are endangered, 12 are vulnerable, and 14 are near threatened. Cluster analyses shows that Chinese mangroves fish were divided into two categories, i.e., coastal mangrove and island mangrove type. This is closely related to the distribution of reef fish. Moreover, the number of fish species showed a strong positive correlation with mangrove area, but not with latitude. The main reasons may be the subtropical and tropical geographic locations, as well as the characteristics of the South China Sea and the Taiwan Warm Current. The size and integrity of mangrove area are crucial to the local ecosystems; thus, protecting and restoring mangroves is of great significance to large-scale ecosystem-stability and local biodiversity.