Changes In Fungal Communities Research Articles

Metabarcoding Reveals Impact of Different Land Uses on Fungal Diversity in the South-Eastern Region of Antioquia, Colombia

Changes in soil fungal communities caused by land use have not been sufficiently studied in South American Andosols, which are considered key food production areas. Since fungal communities play an important role in soil functionality, this study analysed 26 soil samples of Andosols collected from locations devoted to conservation, agriculture and mining activities in Antioquia, Colombia, to establish differences between fungal communities as indicators of soil biodiversity loss using Illumina MiSeq metabarcoding on nuclear ribosomal ITS2 region. A non-metric multidimensional scaling allowed to explore driver factors of changes in fungal communities, while the significance of these variations was assessed by PERMANOVA. Furthermore, the effect size of land use over relevant taxa was quantified. Our results suggest a good coverage of fungal diversity with a detection of 353,312 high-quality ITS2 sequences. We found strong correlations of Shannon and Fisher indexes with dissimilarities on fungal communities (r = 0.94). These correlations allow grouping soil samples according to land use. Variations in temperature, air humidity and organic matter content lead to changes in abundances of relevant orders (Wallemiales and Trichosporonales). The study highlights specific sensitivities of fungal biodiversity features in tropical Andosols, which may serve as a basis for robust assessments of soil quality in the region.

Dynamic changes in soil fungal communities and functional groups in response to sugarcane/soybean intercropping with reduced nitrogen fertilizer application

Dynamic changes in soil fungal communities and functional groups in response to sugarcane/soybean intercropping with reduced nitrogen fertilizer application

Elevated CO2 and temperature increase arbuscular mycorrhizal fungal diversity, but decrease root colonization, in maize and wheat

Anthropogenic climate change threatens ecosystem multifunctionality. Arbuscular mycorrhizal (AM) fungi are important symbionts that participate in mediating many ecosystem processes, and thus being potentially essential link in the chain of responses to climate change. Yet, how climate change affect the abundance and community structure of AM fungi associated with different crops remains elusive. Here, we investigated the changes in rhizosphere AM fungal communities and growth performance of maize and wheat grown in Mollisols under experimentally elevated CO2 (eCO2, +300 ppm), temperature (eT, +2 °C) and both in-combination (eCT) with open-top chambers, representing a scenario likely to occur by this century's end. The results showed that eCT significantly shifted AM fungal communities in both rhizospheres compared with control, but with no remarkable variation of the overall communities in maize rhizosphere, suggesting their greater resistance to climate change. Both eCO2 and eT increased rhizosphere AM fungal diversity, and conversely they reduced mycorrhizal colonization of both crops, probably since AM fungi had distinct adaptive strategies to climate change in rhizospheres (i.e., r-strategy) and roots (K-strategy), while the colonization intensity positively correlated with a decreased phosphorus (P)-uptake in two crops. Furthermore, co-occurrence network analysis showed that eCO2 strongly decreased the modularity and betweenness centrality of network structure than that of eT and eCT in both rhizospheres, along with the reduced network robustness, implied their destabilized communities under eCO2, while root stoichiometry (C:N and C:P ratio) was the most important factor associating with taxa in networks regardless of climate change. Overall, those findings suggest that rhizosphere AM fungal communities in wheat appear to be more sensitive to climate change than that in maize, further highlighting the importance of effective monitoring and managing AM fungi, which may allow crops to maintain critical levels of mineral nutrients (at least P) under future global change.

Changes in fungal community during different phases in conventional and bioreactor composting systems according to metatranscriptomics analysis.

We determined the changes that occurred in fungal community structures and their functions in conventional and bioreactor composting systems. The Illumina MiSeq platform was employed to sequence cDNA by reverse transcription to conduct metatranscriptomics analysis of RNA, and the FUNGuild tool was applied. The α-diversity of fungi in the bioreactor composter increased throughout composting, especially in the initial three phases, but decreased in the conventional composting system. The three dominant phyla in the bioreactor system were Ascomycota (30.27%-68.50%), Mortierellomycota (3.81%-39.51%), and Basidiomycota (9.17%-30.86%). Ascomycota (76.96%-97.18%) was the main phylum in the conventional composting system. Mortierella, Guehomyces, Plectosphaerella, Chaetomium, Millerozyma, and Coprinopsis were the main genera in the bioreactor composter. In the same phase, significant differences in the fungal functions were found between the two composting methods. Available phosphorus was the main factor that affected the community structures and functions of fungi in the bioreactor composter.

Rhizosphere Microbial Community Shows a Greater Response Than Soil Properties to Tea (Camellia sinensis L.) Cultivars

Rhizosphere microbes play pivotal roles in regulating the soil ecosystem by influencing and directly participating in the nutrient cycle. Evidence shows that the rhizosphere microbes are highly dependent on plant genotype and cultivars; however, their characteristics in soils with different tea (Camellia sinensis L.) cultivars are poorly understood. Therefore, the present study investigated the rhizosphere soil properties, microbial community composition, and their potential functions under four tea cultivars Huangjinya (HJY), Tieguanyin (TGY), Zhongcha No.108 (ZC108), and Zijuan (ZJ). The study found a minor impact of cultivars on rhizosphere soil properties but a significant influence on microbial community structure. Except for available potassium (AK) (HJY > TGY > ZC108 > ZJ), tea cultivars had no significant impact on other soil properties. The tea cultivars resulted in substantial differences only in the diversity of soil bacteria of lower taxonomic levels (family to species), as well as significantly changed communities’ structure of bacteria and fungi (R2 = 0.184, p = 0.013 and R2 = 0.226, p = 0.001). Specifically, Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteriota, and Firmicutes accounted for approximately 96% of the bacterial phyla in the tea soils, while Ascomycota, Mortierellomycota, Rozellomycota, Basidiomycota, and Monoblepharomycota (90% of the total) predominated the soil fungal community. Redundancy analysis (RDA) identified soil pH (14.53%) and ammonium-nitrogen (NH4+-N; 16.74%) as the key factors for the changes in bacterial and fungal communities, respectively. Finally, FAPROTAX analysis predicted significant differences in the carbon, nitrogen, and sulfur (C-N-S)-cycling among the soils with different tea cultivars, specifically, ZJ cultivar showed the highest C-cycling but the lowest N- and S-cycling, while FUNGuild analysis revealed that the pathotroph group was significantly lower in ZC108 than the other cultivars. These findings improve our understanding of the differences in microbial community characteristics among tea cultivars and provide a basis for precisely selecting and introducing excellent tea varieties in the agriculture practices.

Distribution characteristics of soil microbial communities and their responses to environmental factors in the sea buckthorn forest in the water-wind erosion crisscross region.

Soil microorganisms are an important part of forest ecosystems, and their community structure and ecological adaptations are important for explaining soil material cycles in the fragile ecological areas. We used high-throughput sequencing technology to examine the species composition and diversity of soil bacterial and fungal communities in sea buckthorn forests at five sites in the water-wind erosion crisscross in northern Shaanxi (about 400 km long). The results are described as follows: (1) The soil bacterial community of the sea buckthorn forest in the study region was mainly dominated by Actinobacteria, Proteobacteria, and Acidobacteria, and the fungi community was mainly dominated by Ascomycota. (2) The coefficient of variation of alpha diversity of microbial communities was higher in the 0-10 cm soil layer than in the 10-20 cm soil layer. (3) Soil electrical conductivity (36.1%), available phosphorous (AP) (21.0%), available potassium (16.2%), total nitrogen (12.7%), and the meteorological factors average annual maximum temperature (33.3%) and average annual temperature (27.1%) were identified as the main drivers of structural changes in the bacterial community. Available potassium (39.4%), soil organic carbon (21.4%), available nitrogen (AN) (13.8%), and the meteorological factors average annual maximum wind speed (38.0%) and average annual temperature (26.8%) were identified as the main drivers of structural changes in the fungal community. The explanation rate of soil factors on changes in bacterial and fungal communities was 26.6 and 12.0%, respectively, whereas that of meteorological factors on changes in bacterial and fungal communities was 1.22 and 1.17%, respectively. The combined explanation rate of environmental factors (soil and meteorological factors) on bacterial and fungal communities was 72.2 and 86.6%, respectively. The results of the study offer valuable insights into the diversity of soil microbial communities in the water-wind erosion crisscross region and the mechanisms underlying their interaction with environmental factors.

Changes of bacterial and fungal communities and relationship between keystone taxon and physicochemical factors during dairy manure ectopic fermentation.

Due to interactions with variety of environmental and physicochemical factors, the composition and diversity of bacteria and fungi in manure ectopic fermentation are constantly changing. The purpose of this study was to investigated bacterial and fungal changes in dairy manure ectopic fermentation, as well as the relationships between keystone species and physicochemical characteristics. Ectopic fermentation was carried out for 93 days using mattress materials, which was combined with rice husk and rice chaff (6:4, v/v), and dairy waste mixed with manure and sewage. Physicochemical characteristics (moisture content, pH, NH4+-N (NN), total organic carbon (TO), total nitrogen (TN) and the C/N ratio) of ectopic fermentation samples were measured, as well as enzymatic activity (cellulose, urease, dehydrogenase and alkaline phosphatase). Furthermore, the bacterial and fungal communities were studied using 16S rRNA and 18S rRNA gene sequencing, as well as network properties and keystone species were analyzed. During the ectopic fermentation, the main pathogenic bacteria reduced while fecal coliform increased. The C/N ratio gradually decreased, whereas cellulase and dehydrogenase remained at lower levels beyond day 65, indicating fermentation maturity and stability. During fermentation, the dominant phyla were Chloroflexi, Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria of bacteria, and Ascomycota of fungi, while bacterial and fungal community diversity changed dramatically and inversely. The association between physicochemical characteristics and community keystone taxon was examined, and C/N ratio was negative associated to keystone genus. These data indicated that microbial composition and diversity interacted with fermentation environment and parameters, while regulation of keystone species management of physicochemical factors might lead to improved maturation rate and quality during dairy manure ectopic fermentation. These findings provide a reference to enhance the quality and efficiency of waste management on dairy farm.

Dysbiotic but nonpathogenic shift in the fecal mycobiota of patients with rheumatoid arthritis

ABSTRACT Rheumatoid arthritis (RA) is closely associated with the oral and gut microbiomes. Fungal cell wall components initiate inflammatory arthritis in mouse models. However, little is known regarding the role of the fungal community in the pathogenesis of RA. To evaluate the association between RA and the gut microbiome, investigations of bacterial and fungal communities in patients with RA are necessary. Therefore, we investigated the compositions and associations of fecal bacterial and fungal communities in 30 healthy controls and 99 patients with RA. The relative abundances of Bifidobacterium and Blautia decreased, whereas the relative abundance of Streptococcus increased, in patients with RA. The relative abundance of Candida in the fecal fungal community was higher in patients with RA than in healthy controls, while the relative abundance of Aspergillus was higher in healthy controls than in patients with RA. Candida species-specific gene amplification showed that C. albicans was the most abundant species of Candida. Ordination analysis and random forest classification models supported the findings of structural changes in bacterial and fungal communities. Aspergillus was the core fecal fungal genus in healthy controls, although Saccharomyces spp. are typically predominant in Western cohorts. In addition, bacterial–fungal association analyses showed that the hub node had shifted from fungi to bacteria in patients with RA. The finding of fungal dysbiosis in patients with RA suggests that fungi play critical roles in the fecal microbial communities and pathogenesis of RA.

Nitrogen deposition and temperature structure fungal communities associated with alpine moss-sedge heath in the UK

Moss-sedge heath, an important habitat of oceanic alpine regions, is under threat from elevated nitrogen (N) deposition and rising temperatures increasing decomposition rates and fragmentation of the extensive, thick moss mats of Racomitrium lanuginosum which characterise this habitat. Here, we examine the potential effects of N deposition and temperature on fungal communities associated with R. lanuginosum mats. Fungal community composition in both green moss shoots and underlying soil were significantly influenced by mat temperatures and green moss shoot N contents. Total OTU, Ascomycota, Basidiomycota and saprotrophic fungal richness in shoots were all positively related to temperature, while in soil, the richness of all groups, except Basidiomycota, was positively related to moss tissue N. The observed community changes suggest that increased N loading and increasing temperatures are ameliorating growing conditions for fungi associated with moss-sedge heath. Further study is required to determine if the observed changes in fungal communities contribute to accelerated decomposition of moss mats and degradation of the habitat. • Alpine moss-sedge heath degradation is linked to N deposition and climate change. • Moss-sedge heath fungal communities are species rich and structured by N deposition and temperature. • Nitrogen enrichment and temperature appear to ameliorate conditions for fungi. • Further studies are required to test possible links between habitat loss and increased fungal species richness.

Elevational distribution patterns and drivers of soil microbial diversity in the Sygera Mountains, southeastern Tibet, China

The Qinghai-Tibet Plateau is one of the most sensitive regions in response to global climate change. Because soil bacteria have a considerable influence on ecosystem function, it is essential to understand their responses to different climates. We investigated the effects of elevation change on soil microbial diversity and community structure in the Abies georgei var. smithii forest of the Sygera Mountains in southeastern Tibet. We sampled soils from 0 to 10 cm depth at 3500 m, 3900 m and 4300 m asl, and examined changes in fungal and bacterial communities using Illumina MiSeq sequencing. The results showed that 1) fungal and bacterial diversity (Shannon index) did not change significantly (P > 0.05) with increasing elevation, and 2) elevation had no effect on the community structure of bacteria but had a significant effect on the community structure of fungi. Redundancy analysis showed that elevation, soil temperature (ST), soil water content (SWC), and total phosphorus (TP) were drivers of changes in fungal community structure. 3) Elevation had no significant effect (P > 0.05) on the relative abundance of the dominant bacterial phylum in the soil but had a significant effect (P < 0.05) on the relative abundance of the dominant fungal phylum. The dominant bacterial phyla were Proteobacteria, Actinobacteria, Acidobacteria, and Choroflexi, whereas the dominant fungal phyla were Basidiomycota, Ascomycota and Mortierllomycota. The relative abundance of Basidiomycota at 3900 m was significantly higher (P < 0.05) than that of Ascomycota at 3500 m and 4300 m, while the relative abundance of Ascomycota at 4300 m was significantly lower (P < 0.05) than that of Basidiomycota at 3500 m and 4300 m. and 4) the complexity of the bacterial network was the lowest at 3900 m elevation, while the most complex at 3500 m elevation. The fungal network complexity was lower than that of the bacteria. In conclusion, soil fungal communities are more sensitive to changes in elevation than are bacterial communities.

Soil microbial communities and their co-occurrence networks in response to long-term Pb-Zn contaminated soil in southern China.

Mining causes extreme heavy metal (HM) contamination to surrounding environments and poses threats to soil microbial community. The effects of HMs on soil microbial communities are not only related to their total amounts but also associated with the distribution of chemical fractions. However, the effects of chemical fractions on soil microbes and their interactions remain largely unclear. Here we investigated soil physicochemical properties and bacterial and fungal communities of soil samples from the control area and lightly (L), moderately (M), and heavily (H) contaminated areas, respectively, which were collected from long-term Pb-Zn slag contamination area in the southern China. The results showed that bacterial and fungal community composition and structure were significantly affected by HMs, while community diversity was not significantly affected by HMs. The critical environmental factor affecting bacterial and fungal communities was pH, and the impacts of chemical fractions on their changes were more significant than the total amounts of HMs. Variance partitioning analysis (VPA) revealed fungal community changes were mostly driven by HM total amounts, but bacterial community changes were mostly driven by soil chemical properties. Co-occurrence network indicated that interactions among species of fungal network were sparser than that of bacterial network, but fungal network was more stable, due to a more significant number of keystone taxa and a lower percentage of positive associations. These illustrated that the fungal community might serve as indicator taxa for HM-contaminated status, and specific HM-responsive fungal species such as Triangularia mangenotii, Saitozyma podzolica, and Cladosporium endophytica, and genus Rhizophagus can be considered relevant bioindicators due to their less relative abundance in contaminated areas. Additionally, HM-responsive bacterial OTUs representing five genera within Sulfurifustis, Thiobacillus, Sphingomonas, Qipengyuania, and Sulfurirhabdus were found to be tolerant to HM stress due to their high relative abundance in contaminated levels.

Fungal Communities in Leaves and Roots of Healthy-Looking and Diseased Ulmusglabra.

The aim of this study was to investigate fungal communities associated with leaves and roots of healthy-looking and declining U. glabra trees. The study was expected to demonstrate whether and how the diversity and composition of fungal communities change in these functional tissues following the infection by Dutch elm disease-causing fungi. The study sites included six U. glabra sites in Lithuania, where leaves and roots were sampled. DNA was isolated from individual samples, amplified using ITS2 rRNA as a marker, and subjected to high-throughput sequencing. The sequence analysis showed the presence of 32,699 high-quality reads, which following clustering, were found to represent 520 non-singleton fungal taxa. In leaves, the fungal species richness was significantly higher in healthy-looking trees than in diseased ones (p < 0.05). In roots, a similar comparison showed that the difference was insignificant (p > 0.05). The most common fungi in all samples of roots were Trichocladium griseum (32.9%), Penicillium restrictum (21.2%), and Unidentified sp. 5238_7 (12.6%). The most common fungi in all samples of leaves were Trichomerium sp. 5238_8 (12.30%), Aureobasidium pullulans (12.03%), Cladosporium sp. 5238_5 (11.73%), and Vishniacozyma carnescens (9.86%). The results showed that the detected richness of fungal taxa was higher in samples collected from healthy-looking trees than from diseased ones, thereby highlighting the negative impact of the Dutch elm disease on the overall fungal diversity.

Synergistic influence on microbial communities ascribed to copper and tetracycline during aerobic composting: Insights into bacterial and fungal structures

There are a considerable number of discussions aimed at analyzing microbial communities and their functions during the composting process. However, microbial succession under copper (Cu) and tetracycline (TCH)-stressed conditions has received less attention. Thus, this work analyzed the bacterial and fungal structures with high-throughput sequencing in Cu/TCH-amended composting (Cu: 0, 100, and 500 mg/kg; TCH: 0, 50, and 300 mg/kg), and the dominating controls on microbial diversity were identified using redundancy analysis (RDA) and structural equation models (SEMs). Low-concentration Cu increased the peak temperature (57°C) at the thermophilic phase. Composting phase-derived changes in bacterial and fungal communities were significant, while Cu and TCH showed a remarkable influence on fungi but not on bacteria. Cu and TCH inhibited Firmicutes' activity while promoting Actinobacteriota growth. Low-concentration Cu and TCH had a negative effect on Basidiomycota in the thermophilic phase and a positive influence on Chytridiomycota in the mature phase. TOC and TN were primary controls on the changes in microbial communities. NH4+-N and NO3--N were more beneficial to fungi with a contribution proportion of 42.13 and 16.85%, respectively. These findings could provide theoretical guidance for the directional research on microbial inoculants.

Responses of Rhizosphere Bacterial and Fungal Communities to the Long-Term Continuous Monoculture of Water Oat.

As an cultivated aquatic vegetable, the long-term continuous monocropping of water oat results in the frequent occurrence of diseases, the deterioration of ecological system and decreased quality of water oat. In this study, real-time quantitative PCR (qPCR) and Illumina high-throughput sequencing were used to determine the dynamic changes in bacterial and fungal communities in rhizosphere soil under continuous cropping of water oat for 1, 5, 10, 15 and 20 years (Y1, Y5, Y10, Y15 and Y20), and soil properties and enzyme activities were also determined. Results showed that the contents of soil organic carbon (SOC), total nitrogen (TN), alkali-hydrolyzable nitrogen (AN), available phosphorus (AP) and the activities of four soil enzymes increased in Y5 and Y10 and then decreased in Y15 and Y20. Spearman correlation analysis identified SOC, TN, AP and AN as the main factors that affect the four enzyme activities. The qPCR results showed that there was no significant difference in bacterial abundance between the different planting years, while the fungal abundance first increased and then decreased. The long-term continuous planting of water oat (Y15 and Y20) significantly reduced the operational taxonomic unit numbers and the Shannon, Chao1, and ACE indices of rhizosphere bacteria and fungi. The bacterial and fungal community compositions were markedly affected by the continuous planting year. The relative abundances of Bacteroidetes and Firmicutes decreased significantly in Y10 and Bacteroidetes increased significantly in Y15. Relative abundances of dominated Mortierellomycota and Ascomycota phyla increased with the continuous cropping years, while Rozellomycota presented the opposite trend. The AK, AN, and SOC were the main factors that changed the bacterial community, while AK and AP significantly shifted the fungal community. Thus, long-term continuous planting of water oat resulted in the deterioration of soil nutrients and microbial communities. The results provided a reference for the remediation of soil under continuous water oat planting and sustainable development of water oat industry.

Changes in Chemical Properties and Fungal Communities of Mineral Soil after Clear-Cutting and Reforestation of Scots Pine (Pinus sylvestris L.) Sites

This study aimed to assess the changes in chemical properties and fungal communities in the upper mineral soil layer in managed Scots pine (Pinus sylvestris L.) ecosystems. Study sites were located in the three largest P. sylvestris massifs in Lithuania, and six sampling sites, representing different development stages of the P. sylvestris forest ecosystem, were selected in each of them: mature P. sylvestris forest stands; clear-cuts of former P. sylvestris mature stand; and the P. sylvestris plantations aging from the 1st to 4th year. High-throughput sequencing was performed to evaluate the soil fungus community at clear-cuts, early-stage reforested sites, and mature forests in Lithuania. This study has shown that, among other chemical soil parameters, the mean concentrations of mineral nitrogen (N), total phosphorus (P), and P2O5 were slightly higher in the clear-cut sites, and significantly higher in the 1st year plantations compared to the mature forests. The quality filtering after PacBio sequencing showed the presence of 60,898 high-quality fungal sequences, and 1143 fungal operational taxonomic units (OTUs). The most abundant fungal OTU in our study was Archaeorhizomyces sp. 5425_1. In total, 70 mycorrhizal fungal OTUs were found in the soil samples at the studied sites. The most abundant ectomycorrhizal fungus identified was Amanita fulva (Schaeff.) Fr. The highest amount of ectomycorrhizal fungal OTUs was found in the clear-cut sites and in the mature forests. The concentrations of mineral N and P2O5 in the upper mineral soil layer did not significantly affect fungal OTUs diversity. Conversely, a relatively strong correlation was obtained between the number of mycorrhizal fungal OTUs and the concentrations of total N and soil organic carbon (SOC), as well as between the numbers of saprotrophic fungal OTUs and the concentration of magnesium ions (Mg2+).

The Changes of Microbial Communities and Key Metabolites after Early Bursaphelenchus xylophilus Invasion of Pinus massoniana.

Pine wood nematode, Bursaphelenchus xylophilus, is a worldwide pest of pine trees, spreading at an alarming rate and with great ecological adaptability. In the process of causing disease, the nematode causes metabolic disorders and changes in the endophytic microbial community of the pine tree. However, the changes at the pine nidus during early nematode invasion have not been well studied, especially the differential metabolites, in Pinus massoniana, the main host of B. xylophilus in China. In this study, we analyzed the endophytic bacterial and fungal communities associated with healthy and B. xylophilus-caused wilted pine trees. The results show that 1333 bacterial OTUs and 502 fungal OTUs were annotated from P. massoniana stem samples. The abundance of bacterial communities in pine trees varies more following infection by B. xylophilus, but the abundance changes of fungal communities are less visible. There were significant differences in endophytic microbial diversity between wilted and healthy P. massoniana. In wilted pine trees, Actinobacteria and Bacteroidia were differential indicators of bacterial communities, whereas, in healthy pine trees, Rhizobiales in the Proteobacteria phylum were the major markers of bacterial communities. Meanwhile, the differential markers of fungal communities in healthy pines are Malasseziales, Tremellales, Sordariales, and Fusarium, whereas Pleosporaceae is the key marker of fungal communities in wilted pines. Our study examines the effect of changes in the endophytic microbial community on the health of pine trees that may be caused by B. xylophilus infection. In parallel, a non-targeted metabolomic study based on liquid mass spectrometry (LC-MS) technology was conducted on pine trees inoculated with pine nematodes and healthy pine trees with a view to identifying key compounds affecting early pine lesions. Ultimately, 307 distinctly different metabolites were identified. Among them, the riboflavin metabolic pathway in pine trees may play a key role in the early pathogenesis of pine wood nematode disease.

Short-Term Vegetation Restoration Enhances the Complexity of Soil Fungal Network and Decreased the Complexity of Bacterial Network.

Different vegetation restoration methods may affect the soil's physicochemical properties and microbial communities. However, it is not known how the microbial network's complexity of the bacterial and fungal communities respond to short-term vegetation restoration. We conducted a short-term ecological restoration experiment to reveal the response of the soil's microbial community and microbial network's stability to initial vegetation restoration during the restoration of the degraded grassland ecosystem. The two restoration methods (sowing alfalfa (Medicago sativa, AF) and smooth brome (Bromus inermis, SB)) had no significant effect on the alpha diversity of the fungal community, but the SB significantly increased the alpha diversity of the soil surface bacterial community (p &lt; 0.01). The results of NMDS showed that the soil's fungal and bacterial communities were altered by a short-term vegetation restoration, and they showed that the available phosphorus (AP), available potassium (AK), and nitrate nitrogen (nitrate-N) were closely related to changes in bacterial and fungal communities. Moreover, a short-term vegetation restoration significantly increased the complexity and stability of fungi ecological networks, but the opposite was the case with the bacteria. Our findings confirm that ecological restoration by sowing may be favorable to the amelioration of soil fungi complexity and stability in the short-term. Such findings may have important implications for soil microbial processes in vegetation recovery.

Circadian rhythms in the plant host influence rhythmicity of rhizosphere microbiota

BackgroundRecent studies demonstrated that microbiota inhabiting the plant rhizosphere exhibit diel changes in abundance. To investigate the impact of plant circadian rhythms on bacterial and fungal rhythms in the rhizosphere, we analysed temporal changes in fungal and bacterial communities in the rhizosphere of Arabidopsis plants overexpressing or lacking function of the circadian clock gene LATE ELONGATED HYPOCOTYL (LHY).ResultsUnder diel light–dark cycles, the knock-out mutant lhy-11 and the gain-of-function mutant lhy-ox both exhibited gene expression rhythms with altered timing and amplitude compared to wild-type plants. Distinct sets of bacteria and fungi were found to display rhythmic changes in abundance in the rhizosphere of both of these mutants, suggesting that abnormal patterns of rhythmicity in the plant host caused temporal reprogramming of the rhizosphere microbiome. This was associated with changes in microbial community structure, including changes in the abundance of fungal guilds known to impact on plant health. Under constant environmental conditions, microbial rhythmicity persisted in the rhizosphere of wild-type plants, indicating control by a circadian oscillator. In contrast, loss of rhythmicity in lhy-ox plants was associated with disrupted rhythms for the majority of rhizosphere microbiota.ConclusionsThese results show that aberrant function of the plant circadian clock is associated with altered rhythmicity of rhizosphere bacteria and fungi. In the long term, this leads to changes in composition of the rhizosphere microbiome, with potential consequences for plant health. Further research will be required to understand the functional implications of these changes and how they impact on plant health and productivity.

Changes in soil fungal communities after onset of wheat yellow mosaic virus disease.

Rhizosphere-associated microbes have important implications for plant health, but knowledge of the association between the pathological conditions of soil-borne virus-infected wheat and soil microbial communities, especially changes in fungal communities, remains limited. We investigated the succession of fungal communities from bulk soil to wheat rhizosphere soil in both infected and healthy plants using amplicon sequencing methods, and assessed their potential role in plant health. The results showed that the diversity of fungi in wheat rhizosphere and bulk soils significantly differed post wheat yellow mosaic virus disease onset. The structure differences in fungal community at the two wheat health states or two compartment niches were evident, soil physicochemical properties (i.e., NH4 +) contribute to differences in fungal community structure and alpha diversity. Comparison analysis showed Mortierellomycetes and Dothideomycetes as dominant communities in healthy wheat soils at class level. The genus Pyronemataceae and Solicoccozyma were significantly are significantly enriched in rhizosphere soil of diseased plant, the genus Cystofilobasidium, Cladosporium, Mortierella, and Stephanonectria are significantly enriched in bulk soil of healthy plant. Co-occurrence network analysis showed that the fungi in healthy wheat soil has higher mutual benefit and connectivity compared with diseased wheat. The results of this study demonstrated that the occurrence of wheat yellow mosaic virus diseases altered both fungal community diversity and composition, and that NH4 + is the most important soil physicochemical factor influencing fungal diversity and community composition.

Indigenous Saccharomyces cerevisiae Could Better Adapt to the Physicochemical Conditions and Natural Microbial Ecology of Prince Grape Must Compared with Commercial Saccharomyces cerevisiae FX10.

Indigenous Saccharomyces cerevisiae, as a new and useful tool, can be used in fermentation to enhance the aroma characteristic qualities of the wine-production region. In this study, we used indigenous S. cerevisiae L59 and commercial S. cerevisiae FX10 to ferment Prince (a new hybrid variety from Lion Winery) wine, detected the basic physicochemical parameters and the dynamic changes of fungal communities during fermentation, and analyzed the correlations between fungal communities and volatile compounds. The results showed that the indigenous S. cerevisiae L59 could quickly adapt to the specific physicochemical conditions and microbial ecology of the grape must, showing a strong potential for winemaking. Compared with commercial S. cerevisiae FX10, the wine fermented by indigenous S. cerevisiae L59 contained more glycerol and less organic acids, contributing to a rounder taste. The results of volatile compounds indicated that the indigenous S. cerevisiae L59 had a positive effect on adding rosy, honey, pineapple and other sweet aroma characteristics to the wine. Overall, the study we performed showed that selection of indigenous S. cerevisiae from the wine-producing region as a starter for wine fermentation is conducive to improving the aroma profile of wine and preserving the aroma of the grape variety.