Soil Fungal Community Composition Research Articles

Enhanced atmospheric nitrogen deposition triggered little change in soil microbial diversity and structure in a desert ecosystem

Enhanced atmospheric nitrogen deposition can greatly influence the soil nitrogen content and soil microorganisms in terrestrial ecosystems. However, there is a lack of knowledge about the response of soil microbes to changes in soil nitrogen, particularly in desert ecosystems. To address this, we used long-term artificial nitrogen addition to simulate atmospheric nitrogen deposition in a desert ecosystem in Ningxia, China. We adopted a high-throughput sequencing method (16S rRNA and ITS) to explore the effects of different amounts of atmospheric nitrogen deposition on soil microbial diversity and community structure. Six years of nitrogen addition (6 g N m −2 y −1 ) significantly increased the soil organic carbon content and the total soil nitrogen content ( p < 0.05) and promoted the growth of Leymus secalinus . However, it did not significantly change the diversity and the structure of soil microbial communities ( p > 0.05). Further analysis revealed that nitrogen addition substantially reduced the number of positive correlations between soil microbial species and the number of core microbial species. Our results suggest that for desert ecosystems, at present, atmospheric nitrogen deposition may increase soil nitrogen use by some vegetation but it does not alleviate the competition for soil nitrogen between soil microbes and vegetation. Moreover, although enhanced atmospheric nitrogen deposition did not significantly change the soil microbial community structure, it may negatively affect the interactions among soil microbial species. This would hinder soil microbial adaptation to the changing environment and the development of desert ecosystems. • The current atmospheric nitrogen deposition cannot significantly change the diversity and structure of microbial community. • Vegetation (e.g. Leymus secalinus ) may be more competitive than soil microorganisms when using soil nitrogen in deserts. • The environmental factors hardly had significant correlations with soil bacterial community composition. • TN, soil pH and SOC had significant correlations with soil fungal community composition. • Enhanced atmospheric nitrogen deposition may negatively affect the interactions among soil microbial species.

Compositional and structural changes in soil microbial communities in response to straw mulching and plant revegetation in an abandoned artificial pasture in Northeast China

The overgrazing and overutilization of pastures can lead to serious degradation that can be restored through proper management practices. However, little is known about the dynamic changes in soil microbial communities during such restoration processes. Therefore, we investigated the characteristics of changes in soil microbial communities during straw mulching and plant revegetation processes in an abandoned artificial pasture in Northeast China. We used 16S rRNA gene and ITS sequencing to analyze the composition and diversity of soil bacterial and fungal communities under control, straw mulching, Leymus chinensis revegetation, and straw mulching + L. chinensis revegetation treatments. Straw mulching was effective in enhancing the contents of total N, alkali-hydrolyzable N, and available P in soils under plant revegetation. The alpha diversity indexes of both bacterial and fungal communities decreased under all treatments. Plant revegetation and straw mulching had an additive effect on the bacterial community composition; their combination increased the absolute abundances of copiotrophic phyla, including Proteobacteria , Actinobacteria , Gemmatimonadetes , Bacteroidetes , and Acidobacteria . However, the response of the fungal community to these treatments was minimal. Moreover, redundancy analysis showed that the soil total N was the most important soil factor affecting the bacterial and fungal community compositions. Our findings highlight the additive effects of straw mulching and revegetation on soil microhabitats and soil bacterial communities, which enhanced the soil quality in an abandoned artificial pasture in Northeast China. • The change characteristics of soil microbial community during the restoration of an abandoned artificial pasture in Northeast China were studied. • The combination of straw mulching and plant revegetation had an additive effect on the soil microbial community composition and diversity as well as on soil properties. • The bacterial community responded more sensitively than the fungal community to restoration, and the bacterial communities changed from oligotrophic to copiotrophic communities. • Soil total nitrogen mainly contributed to explain the bacterial and fungal community compositions.

The distribution of soil fungal communities along an altitudinal gradient in an alpine meadow

Altitude can drive the distribution of living organisms through effects on both soil properties and plant-fungi interactions. We examined how altitude influenced soil fungal communities (including three ecological groups), directly and indirectly through variation in soil properties and/or plant communities, by sampling along an altitudinal gradient from 1300 to 4200 m a.s.l. in an alpine meadow in Western China. We found that soil properties ( r = 0.401; P = 0.001) and plant communities ( r = 0.332; P = 0.001) significantly affected soil fungal community composition. Soil nitrogen content, altitude and nitrate nitrogen content were the best predictors of saprophytic, symbiotic and biotrophic fungi, respectively. Altitude increased the relative abundance (standard coefficient = 0.385) and richness (standard coefficient = 0.689) of soil saprophytic fungi by promoting soil nitrogen content (standard coefficient = 0.574). Altitude directly increased soil symbiotic fungi (standard coefficient = 0.811), while nitrate nitrogen content promoted the richness and abundance of plant fungal pathogens. Our results shed light on drivers of soil fungi community composition and the distribution of different ecological groups along an altitudinal gradient in an alpine meadow.

Soil Fungal Community Composition Correlates with Site-Specific Abiotic Factors, Tree Community Structure, and Forest Age in Regenerating Tropical Rainforests.

Simple SummaryRegenerating forests represent over half of all tropical forests. While regeneration processes of trees and animal groups have been studied, there is surprisingly little information about how the diversity and community composition of fungi and other microorganisms change and what ecological roles play in tropical forest regeneration. In this study, we compared the diversity and community composition of trees and soil fungi among primary forests and regenerating forests of different ages in two sampling areas in southern Costa Rica. Our study shows that while forest age has a significant influence, environmental factors, such as mesoclimate and soil chemistry, have stronger effects on both fungal and tree communities. Moreover, we observed that the more dissimilar tree communities are between any two sites, the more dissimilar the composition of fungal communities. The results presented here contribute to a better understanding of the successional processes of tropical forests in different regions and inform land use and forest management strategies, including, but not limited to, conservation, restoration, and sustainable use.Successional dynamics of plants and animals during tropical forest regeneration have been thoroughly studied, while fungal compositional dynamics during tropical forest succession remain unknown, despite the crucial roles of fungi in ecological processes. We combined tree data and soil fungal DNA metabarcoding data to compare richness and community composition along secondary forest succession in Costa Rica and assessed the potential roles of abiotic factors influencing them. We found a strong coupling of tree and soil fungal community structure in wet tropical primary and regenerating secondary forests. Forest age, edaphic variables, and regional differences in climatic conditions all had significant effects on tree and fungal richness and community composition in all functional groups. Furthermore, we observed larger site-to-site compositional differences and greater influence of edaphic and climatic factors in secondary than in primary forests. The results suggest greater environmental heterogeneity and greater stochasticity in community assembly in the early stages of secondary forest succession and a certain convergence on a set of taxa with a competitive advantage in the more persisting environmental conditions in old-growth forests. Our work provides unprecedented insights into the successional dynamics of fungal communities during secondary tropical forest succession.

Effect of Charcoal on the Properties, Enzyme Activities and Microbial Diversity of Temperate Pine Forest Soils

Relict charcoal hearths (RCHs) increases soil fertility in forest ecosystems. However, the effects of RCHs on the activity and abundance of soil microorganisms remain unknown. In this paper, we analysed the impact of relict charcoal production on the soil enzymatic activity and composition of soil bacterial and fungal communities in Scots pine forests of the Manowo Forest District in northern Poland. Moreover, we determined the effect of relict charcoal production on the soil properties. Our research was conducted by comparing the physical, chemical, enzymatic and microbiological properties of charcoal-enriched and charcoal-free soils. Significant differences in physical properties were found between these two soil types in terms of their structure and water holding capacity. As expected, horizons enriched with charcoal were characterised by a significantly higher organic carbon content (4.7% on average compared to 2.2% in control horizons), and also by a considerably higher content of available phosphorus (an average of 64.07 mg·kg−1 compared to 36.21 mg·kg−1 in the control). Similarly, RCH horizons displayed a higher pH and higher contents of Ca and Na cations. These results indicated that RCH soils provided more favourable conditions for the soil microbiome, as reflected by the higher enzymatic activity and diversity of the microorganisms. Moreover, bacterial and fungal communities in RCH soils were more diverse and had greater species/genera richness, especially in the case of fungi. Members of the genus Rhodoplanes dominated the bacterial community at both RCH and non-RCH sites, followed by Streptomyces, Burkholderia, Skermanella, Tsukamurella and Candidatus Solibacter. Both culture- and next generation sequencing (NGS)-based analyses showed that soil fungal communities were dominated by Ascomycota, with Penicillium as the most abundant genus. Our results showed that hearth soils may represent a significant C pool in the forest ecosystem. This study supports the strategy of safeguarding such charcoal-enriched soils as precious C reservoirs and ecologically important biodiversity hotspots. Moreover, the application of charcoal may effectively increase the microbial diversity of forest soils, especially during the reforestation or re-cultivation of disturbed habitats.

Structure and diversity of fungal communities in long-term copper-contaminated agricultural soil

Copper (Cu) contamination threatens the stability of soil ecosystems. As important moderators of biochemical processes and soil remediation, the fungal community in contaminated soils has attracted much research interest. In this study, soil fungal diversity and community composition under long-term Cu contamination were investigated based on high-throughput sequencing. The co-occurrence networks were also constructed to display the co-occurrence patterns of the soil fungal community. The results showed that the richness and Chao1 index both significantly increased at 50 mg kg−1 Cu and then significantly decreased at 1600 and 3200 mg kg−1 Cu. Soil fungal diversity was significantly and positively correlated with plant dry weight. Specific tolerant taxa under different Cu contamination gradients were illustrated by linear discriminant analysis effect size (LEfSe). Soil Cu concentration and shoot dry weight were the strongest driving factors influencing fungal composition. The relative abundance of arbuscular mycorrhizal fungi increased first and then declined along with elevating Cu concentrations via FUNGuild analysis. The interactions among fungi were enhanced under light and moderate Cu contamination but weakened under heavy Cu contamination by random matrix theory (RMT)-based molecular ecological network analysis. Penicillium, identified as a keystone taxon in Cu-contaminated soils, had the function of removing heavy metals and detoxification, which might be vital to trigger the resistance of the fungal community to Cu contamination. The results may facilitate the identification of Cu pollution indicators and the development of in situ bioremediation technology for contaminated cultivated fields.

Belowground mechanisms for oak regeneration: Interactions among fire, soil microbes, and plant community alter oak seedling growth

It has been firmly established that oak regeneration benefits from prescribed burning and reduced competition with fire-intolerant tree species. Despite recommendations for research on the role of the microsite environment for oak regeneration, very little is known about the interacting effects of fire, soil, and surrounding plant community on oak establishment. We collected undisturbed and burned soil in the aftermath of a wildfire in Great Smoky Mountains National Park and used amplicon sequencing to identify differences in composition of bacterial and fungal communities between unburned and burned soils. To assess the effects of plant community, fire-induced shifts in soil microbial communities, and their interaction we conducted a glasshouse experiment and grew Quercus velutina seedlings in factorial treatments of plant neighbor (oak vs. pine seedling) and soil burn status (unburned vs. burned soil). Fire reduced the diversity of plant pathogenic and saprotrophic fungi and reduced the relative abundance of plant pathogenic fungi. Fire did not affect soil bacterial communities. Shifts in soil fungal community composition enhanced oak seedling root growth, but the effect of the soil microbiome was mediated by plant neighbor interactions. Seedling root growth was negatively correlated with diversity of pathogenic fungi. Root growth was enhanced in burned soil relative to unburned soil, but only when growing with a pine seedling neighbor as opposed to an oak seedling neighbor. Results from this study show that interactions between soil microbes and nearby plants can in part mediate oak seedling growth. As such, nuanced decisions that consider the ecological interactions of the microsite environment are needed to achieve desired outcomes for oak regeneration.

Large-Scale Characterization of the Soil Microbiome in Ancient Tea Plantations Using High-Throughput 16S rRNA and Internal Transcribed Spacer Amplicon Sequencing.

There is a special interaction between the environment, soil microorganisms, and tea plants, which constitute the ecosystem of tea plantations. Influenced by environmental factors and human management, the changes in soil microbial community affected the growth, quality, and yield of tea plants. However, little is known about the composition and structure of soil bacterial and fungal communities in 100-year-old tea plantations and the mechanisms by which they are affected. In this regard, we characterized the microbiome of tea plantation soils by considering the bacterial and fungal communities in 448 soil samples from 101 ancient tea plantations in eight counties of Lincang city, which is one of the tea domestication centers in the world. 16S and Internal Transcribed Spacer (ITS) rRNA high-throughput amplicon sequencing techniques were applied in this study. The results showed that the abundance, diversity, and composition of the bacterial and fungal communities have different sensitivity with varying pH, altitude, and latitude. pH and altitude affect soil microbial communities, and bacterial communities are more sensitive than fungi in terms of abundance and diversity to pH. The highest α-diversity of bacterial communities is shown in the pH 4.50–5.00 and 2,200-m group, and fungi peaked in the pH 5.00–5.50 and 900-m group. Because of environmental and geographical factors, all microbes are similarly changing, and further correlations showed that the composition and structure of bacterial communities are more sensitive than fungal communities, which were affected by latitude and altitude. In conclusion, the interference of anthropogenic activities plays a more important role in governing fungal community selection than environmental or geographical factors, whereas for the bacterial community, it is more selective to environment adaptation than to adaptation to human activities.

Differential Responses of Soil Bacterial and Fungal Community to Short-Term Crop Tree Management in a Larix gmelinii Plantation

Crop tree management (CTM) is a widely applicable silviculture technology that is used to improve the performance of individual trees. However, only little information is available about the effects of the CTM regime on the soil microbial community structure. We conducted a study to explore the effects of short-term (five years) CTM on the soil bacterial and fungal diversity, community composition, and structure in the 0–10 cm soil layer in a Larix gmelinii (Rupr.) Kuzen. plantation. We set out to investigate the differential response of bacterial and fungal communities to variations in soil properties mediated by short-term CTM. Compared with the control plots, the soil microbial biomass carbon and microbial biomass nitrogen in CTM increased significantly by 64.2% and 32.3%, respectively. CTM significantly promoted the content of soil organic carbon, dissolved organic carbon, and nitrate nitrogen, and reduced the content of dissolved organic nitrogen. CTM changed the Shannon and Simpson indices of soil fungi to a remarkable extent but had little effect on the α diversity of bacterial communities. The bacterial β diversity was more sensitive to CTM than fungi. The relative abundance of Verrucomicrobiae (the dominant class of soil bacteria) in CTM was significantly increased by 78.2%, while the relative abundance of Agaricomycetes (dominant class for soil fungi) was reduced by 43.3%. We observed a significantly increased number of unique OTUs for soil fungi in the CTM plots. Redundancy analysis showed that dissolved organic carbon, soil moisture, and total phosphorus content significantly affected the composition of bacterial communities, while soil dissolved organic nitrogen, C/N, and total phosphorus drove the high variation in fungal community composition. Overall, our results emphasize the divergent response of soil bacterial and fungal communities in Larix gmelinii plantations to short-term CTM. We must pay more attention to the functional role of soil microbiota in future forest management.

Diverse compost products influence soil bacterial and fungal community diversity in a potato crop production system

Compost application may be an effective means to rapidly increase soil organic matter, soil quality, and soil microbial community diversity in intensive potato crop production systems. This study compared three contrasting compost products with a no compost control on soil chemical properties and soil bacterial and fungal community composition and diversity. The three composts consisted of municipal source separate waste compost (SSOC), forestry and poultry manure compost (FPMC), and forestry residues waste compost (FRC) with low, medium and high forestry waste percentages in their feedstock, respectively. Soil samples were collected on four dates over 11 months after compost application in October 2014. Soil pH, dissolved organic carbon and readily mineralizable C (respiration) were significantly greater in FPMC- and SSOC-treated soils compared to FRC-treated and control soils. Compost application influenced the relative abundances of several bacterial phyla in soils compared to control soils but not the relative abundances of fungal phyla. Several compost-borne bacterial (average of 383 operational taxonomic units (OTUs)) and fungal (average of 66 OTUs) species could be detected in soil throughout the following growing season after compost product application suggesting that these species succeeded in establishing in soils. The β-diversity of bacterial and fungal communities in soils differed significantly among treatments and sampling dates, indicating that the applied composts resulted in a change in the bacterial and fungal community diversity. Convergence of bacterial community diversity was observed among treatments over time but not for fungal community. The application of diverse compost products clearly changed the soil chemical properties which in turn influenced the bacterial and fungal communities. The effects of compost application on microbial communities were persistent, and could still be observed nearly a year after compost was applied.

Early response of soil fungal communities to the conversion of monoculture cropland to a temperate agroforestry system.

BackgroundAlley-cropping systems in the temperate zone are a type of agroforestry in which rows of fast-growing trees are alternated with rows of annual crops. With numerous environmental benefits, temperate agroforestry is considered a promising alternative to conventional agriculture and soil fungi may play a key in maintaining productivity of these systems. Agroforestry systems that are established for more than 10 years have shown to increase the fungal biomass and impact the composition of soil fungal communities. Investigations of soil fungi in younger temperate agroforestry systems are scarce and the temporal dynamic of these changes is not understood.MethodsOur study was conducted in a young poplar-based alley cropping and adjacent monoculture cropland system in an Arenosol soil in north-west Germany. We investigated the temporal dynamics of fungal populations after the establishment of agroforestry by collecting soil samples half, one, and one and a half years after conversion of cropland to agroforestry. Samples were collected within the agroforestry tree row, at 1, 7, and 24 m distance from the tree row within the crop row, and in an adjacent conventional monoculture cropland. The biomass of soil fungi, Asco-, and Basidiomycota was determined by real-time PCR. Soil fungal community composition and diversity were obtained from amplicon sequencing.ResultsDifferences in the community composition of soil fungi in the tree row and arable land were detected as early as half a year following the conversion of monoculture cropland to agroforestry. In the tree row, soil fungal communities in the plots strongly diverged with the age of the system. The presence of young trees did not affect the biomass of soil fungi.ConclusionsThe composition of soil fungal communities responded rapidly to the integration of trees into arable land through agroforestry, whereas the fungal biomass was not affected during the first one and a half years after planting the trees. Fungal communities under the trees gradually diversified. Adaptation to spatially heterogeneous belowground biomass of the trees and understory vegetation or stochastic phenomena due to limited exchange among fungal populations may account for this effect; long-term monitoring might help unravelling the cause.

Composition and potential functional roles of soil fungal communities on arid farms in Arequipa (Southern Peru) characterized using SMRT sequencing

Small farms near Arequipa, Peru face many challenges including crop diseases caused by soil-borne fungal pathogens. Identifying fungi in these soils and factors that shift the balance between pathogenic and beneficial lifestyles will aid in the development of more effective and sustainable disease control strategies. In this study, the composition and potential functional roles of soil fungal communities on 12 farms was characterized using SMRT sequencing. Communities were compared with soil physiochemical properties and farms grouped based on location (River vs. Canal), and farm age (Old, New, Very New) to investigate possible drivers of community structure and function. Communities were dominated by the Ascomycota phylum, and Fusarium, Alternaria and Cladosporium genera. The majority of phylotypes were saprotrophs, however, an unusually large fraction were pathotrophs (14-29%), and 10% of the entire community were plant pathogens. There were correlations between saprophytic and pathogenic phylotypes with soil pH, organic matter, nitrogen and phosphorous, though the strongest driver of community structure were cobalt and nickel. Dominant pathogenic phylotypes in river and canal farms differed indicating the need for more site-specific intervention strategies. Age was positively correlated with a decline in saprotrophs and increase in pathotrophs highlighting the need to replenish soil organic matter. Correlations between individual phylotypes could mediate disease outbreaks and should be explored in future studies. Results of this study confirm that soils in this unique agroecosystem are highly conducive to the survival of soil-borne pathogens, though it should be possible to suppress these organisms via more targeted soil management practices.

Impact of Soil-Applied Microbial Inoculant and Fertilizer on Fungal and Bacterial Communities in the Rhizosphere of Robinia sp. and Populus sp. Plantations

The impact of chemical fertilization on rhizosphere soil communities is a growing concern due to the changes they cause on microbes in soil ecosystems. The present study aims to compare mycorrhizal inoculation and fertilizer applications on bacterial and fungal communities in rhizosphere soil of intensively cultivated Robinia pseudoacacia and Populus × euramericana plantations using the Illumina Miseq sequencing platform. Our results revealed that the different host plants and applied treatments did not significantly affect soil bacterial diversity, but interfered with native rhizosphere bacterial communities in plantation sites. In contrast, host plants and inorganic fertilizer had a strong effect at the family and genus level on the composition of soil fungal communities. In conclusion, our findings suggest that the structure and composition of the fungal community are more sensitive to the nutrient sources in soil than bacteria.

Effects of Long-Term Bare Fallow During the Winter-Wheat Growth Season on the Soil Chemical Properties, Fungal Community Composition, and the Occurrence of Maize Fungal Diseases in North China.

On the North China Plain, one of the most water-deficient regions in China, bare fallow has been implemented over a large-scale area to conserve water during the growth season of water-intensive winter wheat since 2015. However, the effects of this bare fallow on fungal community and the occurrence of crop diseases are poorly understood. Here we measured soil chemical properties, fungal community composition, and the occurrence of crop diseases after 15 years of long-term fallow (continuous maize or soybean) and non-fallow (maize-wheat rotation; soybean-wheat rotation) cropping systems. Bare fallow during the winter-wheat growth season significantly decreased soil organic matter, available nitrogen, and phosphorus. It also changed the composition of soil fungal communities, i.e., increased relative abundances of some potentially pathogenic species of Lectera, Fusarium, and Volutella but decreased beneficial Cladorrhium and Schizothecium. Meanwhile, the epidemic tendency of maize diseases changed correspondingly: the disease index of southern corn leaf blight and maize brown spot increased, but the incidence of stalk rot decreased compared with the non-fallow system. Soybean diseases were very mild regardless of the cropping system during the total experimental period. Network analysis demonstrated that the soil fungal diversity associated with maize diseases was affected by the decreased soil organic matter and available nitrogen and phosphorus. Our results suggest that bare fallow in the winter-wheat season affected the soil chemical properties, fungal community, and the occurrence of maize fungal diseases.

Suppression of Arbuscular Mycorrhizal Fungi Aggravates the Negative Interactive Effects of Warming and Nitrogen Addition on Soil Bacterial and Fungal Diversity and Community Composition.

We examined the impacts of warming, nitrogen (N) addition, and suppression of arbuscular mycorrhizal fungi (AMF) on soil bacterial and fungal richness and community composition in a field experiment. AMF root colonization and the concentration of an AMF-specific phospholipid fatty acid (PLFA) were significantly reduced after the application of the fungicide benomyl as a soil drench. Warming and N addition had no independent effects but interactively decreased soil fungal richness, while warming, N addition, and AMF suppression together reduced soil bacterial richness. Soil bacterial and fungal species diversity was lower with AMF suppression, indicating that AMF suppression has a negative effect on microbial diversity. Warming and N addition decreased the net loss of plant species and the plant species richness, respectively. AMF suppression reduced plant species richness and the net gain of plant species but enhanced the net loss of plant species. Structural equation modeling (SEM) demonstrated that the soil bacterial community responded to the increased soil temperature (ST) induced by warming and the increased soil available N (AN) induced by N addition through changes in AMF colonization and plant species richness; ST directly affected the bacterial community, but AN affected both the soil bacterial and fungal communities via AMF colonization. In addition, higher mycorrhizal colonization increased the plant species richness by increasing the net gains in plant species under warming and N addition. IMPORTANCE AMF can influence the composition and diversity of plant communities. Previous studies have shown that climate warming and N deposition reduce the effectiveness of AMF. However, how AMF affect soil bacterial and fungal communities under these global change drivers is still poorly understood. A 4-year field study revealed that AMF suppression decreased bacterial and fungal diversity irrespective of warming or N addition, while AMF suppression interacted with warming or N addition to reduce bacterial and fungal richness. In addition, bacterial and fungal community compositions were determined by mycorrhizal colonization, which was regulated by soil AN and ST. These results suggest that AMF suppression can aggravate the severe losses to native soil microbial diversity and functioning caused by global changes; thus, AMF play a vital role in maintaining belowground ecosystem stability in the future.

Effects of addition of sorghum stubble rhizosphere soil on growth and rhizosphere microbes of continuous cropping cucumber

We explored the effects of addition of sorghum stubble rhizosphere soil on the growth of continuous cropping cucumber and rhizosphere microbial community in a pot experiment. The diffe-rences in soil bacterial and fungal community composition were analyzed with fluorescence quantitative PCR and high-throughput sequencing technology. There were four treatments: CK (no fertilization), T1(fertilizer only), T2(optimized fertilization), and T3(optimized fertilization + rhizosphere soil of sorghum stubble). The results showed that compared with other treatments, T3 promoted the growth and development of cucumber, and increased the abundance of 16S rRNA and ITS rRNA genes in soil. Compared with the T1 treatment, T2 and T3 significantly increased the richness and diversity of bacterial communities. There was no significant difference in fungal community richness and diversity among different treatments. Adding rhizosphere soil of sorghum stubble changed the composition of bacterial and fungal communities at both phylum and genus levels. For bacteria, it increased the abundances of Acidobacteria and Bacteroides, but decreased that of Proteobacteria, Firmicutes, Nitrospira and Bacillus. For fungi, it increased the abundance of Basidiomycota, Trichoderma and Pseudurotium, but decreased that of Fusarium and Metarhizium. Results of redundancy analysis showed that soil nitrate and organic matter were the key factors affecting the difference of bacterial and fungal community composition, respectively. In conclusion, addition of sorghum stubble rhizosphere soil improved the total abundance of soil microorganisms and bacterial diversity for continuous cropping cucumber. It increased the abundance of beneficial bacteria Trichoderma, reduced that of pathogenic Fusarium, and maintained the survival rate of cucumber, thus provided a feasible solution for alleviating the barriers for the continuous cropping of cucumber.

Influence of Tall Fescue Epichloë Endophytes on Rhizosphere Soil Microbiome.

Tall fescue (Lolium arundinaceum (Schreb.) S.J. Darbyshire) often forms a symbiotic relationship with fungal endophytes (Epichloë coenophiala), which provides increased plant performance and greater tolerance to environmental stress compared to endophyte-free tall fescue. Whether this enhanced performance of tall fescue exclusively results from the grass–fungus symbiosis, or this symbiosis additionally results in the recruitment of soil microbes in the rhizosphere that in turn promote plant growth, remain a question. We investigated the soil bacterial and fungal community composition in iron-rich soil in the southeastern USA, and possible community shifts in soil microbial populations based on endophyte infection in tall fescue by analyzing the 16s rRNA gene and ITS specific region. Our data revealed that plant-available phosphorus (P) was significantly (p < 0.05) influenced by endophyte infection in tall fescue. While the prominent soil bacterial phyla were similar, a clear fungal community shift was observed between endophyte-infected (E+) and endophyte-free (E−) tall fescue soil at the phylum level. Moreover, compared to E− soil, E+ soil showed a greater fungal diversity at the genus level. Our results, thus, indicate a possible three-way interaction between tall fescue, fungal endophyte, and soil fungal communities resulting in improved tall fescue performance.

Effects of Biogas Slurry Combined With Chemical Fertilizer on Soil Bacterial and Fungal Community Composition in a Paddy Field.

The application of biogas slurry and chemical fertilizer in paddy fields can be a practical method to reduce the environmental risk and utilize the nutrients of biogas slurry. The responses of bacterial and fungal communities to the application of biogas slurry and chemical fertilizer are important reflections of the quality of the ecological environment. In this study, based on a 3-year field experiment with different ratios of biogas slurry and chemical fertilizer (applying the same pure nitrogen amount), the Illumina MiSeq platform was used to investigate the bacterial and fungal community diversity and composition in paddy soil. Our results revealed that compared with the observations under regular chemical fertilization, on the basis of stable paddy yield, the application of biogas slurry combined with chemical fertilizer significantly enhanced the soil nutrient availability and bacterial community diversity and reduced the fungal community diversity. Dissolved organic carbon (DOC), DOC/SOC (soil organic carbon), available nitrogen (AN) and available phosphorus (AP) were positively correlated with the bacterial community diversity, but no soil property was significantly associated with the fungal community. The bacterial community was primarily driven by the application of biogas slurry combined with chemical fertilizer (40.78%), while the fungal community was almost equally affected by the addition of pure biogas slurry, chemical fertilizer and biogas slurry combined with chemical fertilizer (25.65–28.72%). Biogas slurry combined with chemical fertilizer significantly enriched Proteobacteria, Acidobacteria, Planctomycetes, Rokubacteria, and Ascomycota and depleted Chloroflexi, Bacteroidetes, Crenarchaeota, Basidiomycota, and Glomeromycota. The observation of the alteration of some bacteria- and fungus-specific taxa provides insights for the proper application of biogas slurry combined with chemical fertilizer, which has the potential to promote crop growth and inhibit pathogens.

Changes in soil bacterial and fungal community composition and functional groups during the succession of boreal forests

Clarifying the response of soil microbial communities and their potential functions during succession is of great significance for understanding the biogeochemical processes and the sustainability of forest development. However, the study of microbial community dynamics during the process of succession remains poorly understood in boreal forest ecosystems. Thus, in order to study the dynamics of microbial diversity caused by succession, we adopted the "space instead of time" method and selected four habitats in a national natural reserve (including grassland, birch forest, mixed forest and larch forest) to represent the primary successional sequence of the boreal forest. We used 16S and ITS rRNA gene sequencing to detect bacterial and fungal communities and used FAPROTAX and FUNGuild database to predict bacterial and fungal functional groups. The results showed that forest succession significantly changed the community composition of bacteria and fungi, among which the fungal community was more sensitive to the changes with successional stage. The relative abundance of ectomycorrhizal fungi significantly increased with succession, while the relative abundance of bacterial functional groups involved in the nitrogen cycle did not change significantly, indicating that fungi might play a major regulatory role in the nutrient cycling process during the successional process. In this study, the soil total carbon and total nitrogen were the dominating factors affecting the soil microbial community and the structure of fungal functional groups. Our results suggest that the shifts in fungal community structure and functional groups may play a key role in soil nutrient cycling during boreal ecosystems succession.

Lower relative abundance of ectomycorrhizal fungi under a warmer and drier climate is linked to enhanced soil organic matter decomposition.

The aboveground impacts of climate change receive extensive research attention, but climate change could also alter belowground processes such as the delicate balance between free-living fungal decomposers and nutrient-scavenging mycorrhizal fungi that can inhibit decomposition through a mechanism called the Gadgil effect. We investigated how climate change-induced reductions in plant survival, photosynthesis and productivity alter soil fungal community composition in a mixed arbuscular/ectomycorrhizal (AM/EM) semiarid shrubland exposed to experimental warming (W) and/or rainfall reduction (RR). We hypothesised that increased EM host plant mortality under a warmer and drier climate might decrease ectomycorrhizal fungal (EMF) abundance, thereby favouring the proliferation and activity of fungal saprotrophs. The relative abundance of EMF sequences decreased by 57.5% under W+RR, which was accompanied by reductions in the activity of hydrolytic enzymes involved in the acquisition of organic-bound nutrients by EMF and their host plants. W+RR thereby created an enhanced potential for soil organic matter (SOM) breakdown and nitrogen mineralisation by decomposers, as revealed by 127-190% increases in dissolved organic carbon and nitrogen, respectively, and decreasing SOM content in soil. Climate aridification impacts on vegetation can cascade belowground through shifts in fungal guild structure that alter ecosystem biogeochemistry and accelerate SOM decomposition by reducing the Gadgil effect.