Fungal Co-occurrence Network Research Articles

Effects of Microbial Organic Fertilizer, Microbial Inoculant, and Quicklime on Soil Microbial Community Composition in Pepper (Capsicum annuum L.) Continuous Cropping System

The additions of microbial organic fertilizer (MOF), a microbial inoculant (MI), and quicklime (Q) are considered to be sustainable practices to restore land that has been damaged by continuous cropping of pepper (Capsicum annuum L.). However, the combined effects of these three additives on pepper yield, soil chemical properties, and soil microbial communities were unclear. The experimental design consists of 13 treatment groups: the untreated soil (control); soil amended solely with three treatments for each of MOF (1875–5625 kg ha−1), MI (150–450 mL plant−1), and Q (1500–4500 kg ha−1); and soil amended with combinations of MOF, MI, and Q at three comparable concentrations. A significant increase in pepper fruit diameter, length, yield, and soil available nitrogen, phosphorus, and potassium contents occurs upon exclusive and combined applications of MOF, MI, and Q. Pepper yield was greatest (29.89% more than control values) in the combined treatment with concentrations of 1875 kg ha−1 MOF, 150 mL plant−1 MI, and 1500 kg ha−1 Q. The application of Q increased soil pH and reduced soil–fungal richness. The application of MOF, MI, and Q increased the relative abundance of bacterial genera and the complexity of bacterial and fungal co-occurrence networks compared with control levels. The combined application of MOF, MI, and Q resulted in the greatest microbial network complexity. A Mantel test revealed the key role of soil available nitrogen content and bacterial diversity in the regulation of pepper growth and yield. We conclude that the combined application of MOF, MI, and Q improves soil nutrient availability and modifies soil microbial community composition, significantly promoting plant growth and pepper yield during continuous cultivation.

Eucalyptus and Native Broadleaf Mixed Cultures Boost Soil Multifunctionality by Regulating Soil Fertility and Fungal Community Dynamics.

The growing recognition of mixed Eucalyptus and native broadleaf plantations as a means of offsetting the detrimental impacts of pure Eucalyptus plantations on soil fertility and the wider ecological environment is accompanied by a clear and undeniable positive impact on forest ecosystem functions. Nevertheless, the question of how mixed Eucalyptus and native broadleaf plantations enhance soil multifunctionality (SMF) and the mechanisms driving soil fungal communities remains unanswered. In this study, three types of mixed Eucalyptus and native broadleaf plantations were selected and compared with neighboring evergreen broadleaf forests and pure Eucalyptus plantations. SMF was quantified using 20 parameters related to soil nutrient cycling. Partial least squares path modeling (PLS-PM) was employed to identify the key drivers regulating SMF. The findings of this study indicate that mixed Eucalyptus and native broadleaf plantations significantly enhance SMF. Mixed Eucalyptus and native broadleaf plantations led to improvements in soil properties (7.60-52.22%), enzyme activities (10.13-275.51%), and fungal community diversity (1.54-29.5%) to varying degrees compared with pure Eucalyptus plantations. Additionally, the mixed plantations exhibit enhanced connectivity and complexity in fungal co-occurrence networks. The PLS-PM results reveal that soil properties, fungal diversity, and co-occurrence network complexity directly and positively drive changes in SMF. Furthermore, soil properties exert an indirect influence on SMF through their impact on fungal diversity, species composition, and network complexity. The findings of this study highlight the significant role of mixed Eucalyptus and native broadleaf plantations in enhancing SMF through improved soil properties, fungal diversity, and co-occurrence network complexity. This indicates that incorporating native broadleaf species into Eucalyptus plantations can effectively mitigate the negative impacts of monoculture plantations on soil health and ecosystem functionality. In conclusion, our study contributes to the understanding of how mixed plantations influence SMF, offering new insights into the optimization of forest management and ecological restoration strategies in artificial forest ecosystems.

Microbial inoculants using spent mushroom substrates as carriers improve soil multifunctionality and plant growth by changing soil microbial community structure

Peat is typically used as a carrier for microbial inoculants; however, due to its non-renewable nature alternatives need to be identified as reliable and renewable carriers for mineral-solubilizing inoculants. In pot experiments, solid microbial inoculants were comprised of peat (P), biochar (BC), and spent mushroom substrates (SMS) using Medicago sativa L. as experimental materials, and the purpose of this study is to assess the effect of solid microbial inoculants on soil multifunctionality and plant growth. The results revealed that the SMS microbial inoculant had the greatest positive impact on plant biomass and significantly stimulated soil multifunctionality which is typically managed or assessed based on various soil functions or processes that are crucial for sustaining productivity, in contrast to the peat microbial inoculant, particularly at a supply level of 100 g/pot. There was no significant correlation between soil multifunctionality and bacterial/fungal microbial diversity. However, according to the co-occurrence network of bacteria and fungi, soil multifunctionality was intimately correlated with the biodiversity of the main ecological clusters (modules) of bacteria and fungi, rather than to the entire soil microbial community structure. The keystone species of module hubs and connectors play critical roles in maintaining the stability of ecological clusters of microbial co-occurrence networks and linkages between ecological clusters. Soil pH is a major predictor of changes in plant biomass, and leads to changes therein by affecting the major ecological clusters of bacterial and fungal co-occurrence networks. These results suggested that SMS may serve as a good alternative to peat as a carrier of mineral-solubilizing microorganisms to maintain soil multifunctionality and promote plant growth.

Linking main ecological clusters of soil bacterial–fungal networks and nitrogen cycling genes to crop yields under diverse cropping systems in the North China Plain

BackgroundCrop rotation changes crop species and the associated management strategies, significantly influencing soil fertility and soil microbial communities. Interactions among the species in microbial communities are important for soil nutrient cycling. Yet, the contribution of soil microbial interactions to crop yield and soil nitrogen-cycle function under wheat–maize and wheat–soybean rotation conversion remains unclear. An 8-year field experiment was conducted to investigate the impact of simple [8-year wheat–maize rotation (8WM) and 8-year wheat–soybean rotation (8WS)] and diverse cropping systems [4-year wheat–soybean followed by 4-year wheat–maize rotation (4WS4WM) and 4-year wheat–maize followed by 4-year wheat–soybean rotation (4WM4WS)] on crop yield, soil properties, bacterial–fungal co-occurrence networks and nitrogen functional potentials. The abundances of genes with nitrogen fixation (nifH), nitrification (AOB and nxrA) and denitrification (narG, nirK, norB and nosZ) potentials were quantified and bacterial and fungal communities were characterized.Results4WS4WM led to higher succeeding maize yields and lower bacterial–fungal network complexity, nitrogen fixation potentials and denitrifying potentials than 8WM. Meanwhile, 4WM4WS exhibited higher succeeding wheat and soybean yields, network complexity and lower nitrifying potentials than 8WS. The ecological cluster with the most nitrifying and denitrifying bacterial species (Module#5) and that with the least species (Module#3) dominated the potentials of nitrogen fixation, nitrification and denitrification and succeeding maize yields in 4WS4WM and 8WM. Module#4 with the highest abundances of nitrifying bacteria (Nitrosomonadaceae) and Module#2 with the most species dominated the nitrifying potentials and succeeding wheat and soybean yields in 4WM4WS and 8WS. Soil water content, organic carbon, dissolved organic carbon, NO3− and pH were key drivers influencing Module#3 and Module#5, while only NH4+ significantly affected Module#2 and Module#4.ConclusionsThese findings demonstrate the importance of ecological clusters within soil microbial network in regulating crop yield and soil nitrogen cycling, and identify specific ecological clusters dominating nitrogen functional potentials in wheat–maize and wheat–soybean rotations, offering science-based recommendations for sustainable crop rotation practices.Graphical

Revealing the microbial composition changes and relationship with Fusarium caused by rot disease in the Crocus sativus L.

PurposeRot disease caused by Fusarium poses a formidable threat to the growth of saffron (Crocus sativus L.), resulting in substantial damage to both yield and quality. It is paramount to delve into the root causes of rot disease in saffron to optimize both yield and quality. Existing preventive and treatment modalities have exerted deleterious effects on corms and the natural environment. Consequently, the quest for efficacious and eco-friendly methods such as biological control agents has become an urgent imperative.MethodsThe disparate distribution of microbial communities between rhizospheric microorganisms and saffron serves as the foundational exploration for uncovering the underlying causes of rot disease. Samples from various saffron organs and rhizosphere soil were gathered, and the sequencing data from the microbial communities were interpreted using 16S rRNA and ITS gene sequencing methods. This facilitated an in-depth examination of the composition and changes of microorganisms in both healthy and diseased saffron plants.ResultsThe findings indicated rot disease reduced the abundance and diversity of microorganisms in saffron, and the fungal co-occurrence networks were less stable and their communities were more sensitive to rot disease than the bacterial community. Fusarium was the predominant genus in diseased samples, accounting for 99.19% and 89.77% of the communities in diseased leaves and corms. With corms and leaves displaying heightened susceptibility to infection compared to other plant organs. Some of the beneficial bacterial taxa enriched in the diseased plants were also identified in networks, they showed an antagonistic relationship with Fusarium, suggesting a potential for these bacteria to be used in biologically based control strategies against rot disease. These insights could prove invaluable for the development of biocontrol agents aimed at combating this plant ailment.ConclusionThese findings significantly advance our understanding of saffron-microbiome interactions and could provide fundamental and important data for improving saffron yield and quality in the process of sustainable development.

Soil Fungal Community Differences in Manual Plantation Larch Forest and Natural Larch Forest in Northeast China.

Soil fungal communities are pivotal components in ecosystems and play an essential role in global biogeochemical cycles. In this study, we determined the fungal communities of a natural larch forest and a manual plantation larch forest in Heilongjiang Zhongyangzhan Black-billed Capercaillie Nature Reserve and Gala Mountain Forest using high-throughput sequencing. The interactions between soil fungal communities were analysed utilising a co-occurrence network. The relationship between soil nutrients and soil fungal communities was determined with the help of Mantel analysis and a correlation heatmap. The Kruskal-Wallis test indicated that different genera of fungi differed in the two forest types. The results show that there was a significant change in the alpha diversity of soil fungal communities in both forests. In contrast, nonmetric multidimensional scaling (NMDS) analysis showed significant differences in the soil fungal community structures between the manual plantation larch forest and the natural larch forest. The soil fungal co-occurrence network showed that the complexity of the soil fungal communities in the manual plantation larch forest decreased significantly compared to those in the natural larch forest. A Mantel analysis revealed a correlation between the soil fungal co-occurrence network, the composition of soil fungi, and soil nutrients. The RDA analysis also showed that AN, TK, and pH mainly influenced the soil fungal community. The null model test results showed the importance of stochastic processes in soil fungal community assembly in manual plantation larch forests. Overall, this study enhances our understanding of the differences in soil fungal communities in manual plantation larch forests and natural larch forests, providing insights into their sustainable management. It also serves as a reminder that the ecological balance of natural ecosystems is difficult to restore through human intervention, so we need to protect natural ecosystems.

Distinct planting patterns exert legacy effects on the networks and assembly of root-associated microbiomes in subsequent crops

Soil legacy effects from previous crops can significantly influence plant–soil interactions in crop rotations. However, the microbial mechanism underlying this effect in subsequent root-associated compartments remains unclear. We investigated the effects of planting patterns (four-year continuous maize [MM], three-year winter wheat and one-year maize rotation [WM], and three-year potato and one-year maize rotation [PM]) on the microbial composition and structure of root-associated compartments, the effect of distinct crops on subsequent microbial co-occurrence patterns, and the assembly mechanism by which the root-associated compartments (bulk soil, rhizosphere, and roots) in subsequent crops regulate the microbiome habitat. Compared with MM, the relative abundance of Acidobacteria in WM was 29.7 % lower, whereas that of Bacteroidota in PM was 37.9 % higher in all three compartments. The co-occurrence patterns of the microbial communities exhibited varied responses to different planting patterns. Indicator taxon analysis revealed less shared and specific species in the root bacterial and fungal networks. The planting pattern elicited specific responses from modules within bacterial and fungal co-occurrence networks in all three compartments. Moreover, the planting patterns and root-associated compartments collectively drove the assembly process of root-associated microorganisms. The neutral model showed that, compared with MM, the stochasticity of bacterial assembly decreased under WM and PM but increased for fungal assembly. WM and PM increased the relative effects of the homogenized dispersal of fungal assemblies in roots. We conclude that previous crops exhibit marked legacy effects in the root-associated microbiome. Therefore, soil heritage should not be ignored when discussing microbiome recruitment strategies and co-occurrence patterns in subsequent crops.

Sporocarp-associated fungal co-occurrence networks in a corn field revealed by long-read high-throughput sequencing

Sporocarp-associated fungal co-occurrence networks in a corn field revealed by long-read high-throughput sequencing

Plant compartment niche is more important in structuring the fungal community associated with alpine herbs in the subnival belt of the Qiangyong glacier than plant species

The plant compartment niche (i.e., the host plant provides various microhabitats for the microbial community, such as the rhizosphere, root endosphere, leaf endosphere, and phylloplane) and plant species play a significant role in shaping the plant-associated microbial community assembly. However, in the mycobiome associated with alpine herbs in the subnival belt research, little work has been done to assess the contribution of plant compartment niches and plant species to fungal community variation and to reveal the plant compartment niche differentiation of fungal communities. In this study, we quantified the fungal communities associated with the rhizosphere soil, root endospheres, and leaf endospheres of three alpine herbs (Rheum spiciforme, Eriophyton wallichii, and Rhodiola bupleuroides) in the subnival belt of the Qiangyong glacier using high-throughput DNA sequencing. Our results revealed that the variation in diversity and composition of the fungal community was predominantly shaped by plant compartment niche rather than plant species. Rhizosphere soil exhibited the highest level of fungal diversity and niche breadth, while the lowest level was observed in the leaf endosphere. The fungal community composition significantly differed across different plant compartment niches. Fungal co-occurrence networks of the root endosphere and leaf endosphere were more complex and showed higher centrality and connectedness than the rhizosphere soil. Moreover, we also found that the deterministic process governed the fungal community assembly, and the host plant exerts stronger selection pressure on the leaf endophytes in comparison with the root endophytes. The root endophytes are the primary potential contributors to the leaf endophytes, compared with the fungal community associated with rhizosphere soil. Further, the Pleosporaceae, Davidiellaceae, and Chaetomiaceae were significantly enriched and overlapped in two plant compartment niches (root endosphere and leaf endosphere). Collectively, this study reveals that the variation in the diversity and composition of fungal communities associated with three alpine herbs were primarily affected by plant compartment niches rather than plant species. Additionally, this study also reveals that the diversity, composition, co-occurrence pattern, and assembly process of fungal communities associated with three alpine herbs exhibited plant compartment niche differentiation. These results provide a novel insight into the community assembly and ecological interactions of fungal communities associated with plants in harsh environments.

Novel insights into the rhizosphere and seawater microbiome of Zostera marina in diverse mariculture zones

BackgroundSeagrasses offer various ecosystem services and possess high levels of primary productivity. However, the development of mariculture has affected the homeostasis of seagrass meadow ecosystems. Plant-microbiome associations are essential for seagrasses health, but little is known about the role of environmental microbiomes and how they affect seagrass in a mariculture environment. In this study, we investigated the influence of mariculture on the rhizosphere and seawater microbiome surrounding Zostera marina and focused on the bacterial, eukaryotic, and fungal components in the composition, diversity, metabolism, and responses to mariculture-related environmental factors.ResultsSignificant differences in the composition, richness, diversity, and internal relations of the bacterial community between the seawater and rhizosphere sediment surrounding Z. marina were observed, while differences in the eukaryotic and fungal communities were less significant. More complex bacterial and fungal co-occurrence networks were found in the seawater and rhizosphere sediment of the Saccharina japonica (SJ) and sea cucumber (SC) culture zones. The seawater in the SJ zone had higher levels of dissimilatory and assimilatory nitrate reduction, denitrification, and nitrogen fixation processes than the other three zones. The assimilatory sulfate reduction enzymes were higher in the rhizosphere sediments of the SJ zone than in the other three zones. Tetracycline, sulfonamide, and diaminopyrimidine resistance genes were enriched in the mariculture SJ and SC zones.ConclusionsOur findings might contribute to a better understanding of the effects of mariculture on the seagrass and the meadow ecosystems and thus revealing their potential operating mechanisms. These insights may serve to raise awareness of the effects of human activities on natural ecosystems, regulation of antibiotic usage, and environmental restoration.7tqXcmUUPbCQ9vMfWLp9EQVideo

Interactions of rhizosphere microbiota-environmental factors-pharmacological active ingredients of Eucommia ulmoides.

The composition, diversity and co-occurrence patterns of the rhizosphere microbiota of E. ulmoides were significantly influenced by environmental factors, and which were potentially associated with the contents of pharmacological active ingredients. Eucommia ulmoides is an important perennial medicinal plant. However, little is known about the interactions among microbiota, environmental factors (EFs), and pharmacological active ingredients (PAIs) of E. ulmoides. Herein, we analyzed the interactions among rhizosphere microbiota-EFs-PAIs of E. ulmoides by amplicon sequencing and multi-analytical approach. Our results revealed variations in the dominant genera, diversity, and co-occurrence networks of the rhizosphere microbiota of E. ulmoides across different geographical locations. Notably, available nitrogen exerted the strongest influence on fungal dominant genera, while pH significantly impacted bacterial dominant genera. Rainfall and relative humidity exhibited pronounced effects on the α-diversity of fungal groups, whereas available phosphorus influenced the number of nodes in fungal co-occurrence networks. Altitude and total phosphorus had substantial effects on the average degree and nodes in bacterial co-occurrence networks. Furthermore, the dominant genera, diversity and co-occurrence network of rhizosphere microbiota of E. ulmoides were significantly correlated with the content of PAIs. Specifically, the abundance of rhizosphere dominant genera Filobasidium, Hannaella and Nitrospira were significantly correlated with the content of pinoresinol diglucoside (PD). Similarly, the abundance of Vishniacozyma and Bradyrhizobium correlated significantly with the content of geniposidic acid (GC), while the abundance of Gemmatimonas was significantly correlated with the content of aucubin. Moreover, the bacterial co-occurrence network parameters including average degree, density, and edge, were significantly correlated with the content of GC and aucubin. The α-diversity index Chao1 also displayed a significant correlation with the content of PD. These findings contribute to a more comprehensive understanding of the interactions between medicinal plants and microbes.

Plant–soil feedback is dependent on tree mycorrhizal types and tree species richness in a subtropical forest

Plant-soil feedback (PSF) is an important driver of plant species coexistence and diversity maintenance. However, it remains unclear how changes in PSF due to decline in tree species richness influence the performance of arbuscular mycorrhizal (AM) and ectomycorrhizal (EcM) tree species. A PSF experiment was established with eight target tree species (four AM and four EcM tree species) based on a subtropical forest Biodiversity-Ecosystem Functioning Experimental in China (BEF-China) platform, where soil inocula were collected beneath the canopy of target tree species individuals growing in monoculture and eight tree-species mixture plots. We hypothesized that the negative PSF strength of AM tree species would be stronger in monocultures than that in eight tree-species mixtures, resulting in better performance in highly diverse plant communities, whereas EcM tree species would benefit less from tree species richness. However, the results showed consistent PSFs of AM tree species regardless of tree species richness. In contrast, EcM tree species experienced a change from positive in monocultures to negative PSF in eight tree-species mixtures, influencing the performance of EcM tree seedlings. With high concern of the cascading effects of tree species richness on PSFs via modulating soil fungal communities, we revealed that the alterations in EcM fungal abundance, putatively pathogenic fungal diversity, and fungal co-occurrence network complexity mirrored those of PSF associated with EcM tree species, showing the changes from positive in monocultures to negative feedback in eight tree-species mixtures. Our findings highlight the differential PSFs exhibited by AM and EcM tree species in response to tree species richness, and provide insight into the potential role of fungal functional guilds and co-occurrence network complexity in shaping the PSFs of them.

Increased precipitation alters the effects of nitrogen deposition on soil bacterial and fungal communities in a temperate forest

Anthropogenic nitrogen (N) deposition and increased precipitation are known to alter soil microbial communities. However, the combined effects of elevated N deposition and increased precipitation on soil microbial community dynamics and co-occurrence networks in temperate forests remain elusive. In this study, we conducted a field manipulation experiment by applying N solution and water to the forest canopy to simulate natural N deposition and increased precipitation in a temperate forest. We collected samples in the litter layer, organic soil layer, and mineral soil layer in 2018–2019 after 6–7 years of N and water treatments, and explored how elevated N deposition and increased precipitation regulate soil microbial diversity, community composition, and co-occurrence networks in different soil layers and at different sampling times. We found that the effects of N deposition and increased precipitation on soil microbial communities varied with soil layers and sampling times. Compared to the ambient environment, single canopy N addition (CN) or single canopy water addition (CW) did not affect bacterial Shannon diversity in the mineral soil layer in 2018, but the combined canopy N and water additions (CNW) decreased it in this layer at this time. CN increased fungal OTU richness in the organic and mineral soil layers in 2018; however, CW and CNW did not have an effect on it in the same layer at the same time. CW and CNW, but not CN, significantly affected bacterial and fungal community compositions in the litter layer in 2018 and in the organic soil layer in 2019. In contrast, CN, but not CW or CNW, significantly affected fungal community composition in the litter layer in 2019. CNW exhibited higher complexities of bacterial and fungal co-occurrence networks than CN and the ambient environment, indicating increased precipitation can strengthen the effect of N deposition on the complexity of bacterial and fungal co-occurrence networks. Our findings suggest that increased precipitation alters the effects of atmospheric N deposition on soil bacterial and fungal communities in this temperate forest, depending on soil layer and sampling time. Moreover, both bacterial and fungal community compositions are sensitive to increased precipitation, but the bacterial community composition is more sensitive to N deposition than the fungal community composition in the organic and mineral soil layers in this forest.

Resistance mechanisms of cereal plants and rhizosphere soil microbial communities to chromium stress.

Agricultural soils contaminated with heavy metals poison crops and disturb the normal functioning of rhizosphere microbial communities. Different crops and rhizosphere microbial communities exhibit different heavy metal resistance mechanisms. Here, indoor pot studies were used to assess the mechanisms of grain and soil rhizosphere microbial communities on chromium (Cr) stress. Millet grain variety 'Jingu 21' (Setaria italica) and soil samples were collected prior to control (CK), 6 hours after (Cr_6h), and 6 days following (Cr_6d) Cr stress. Transcriptomic analysis, high-throughput sequencing and quantitative polymerase chain reaction (qPCR) were used for sample determination and data analysis. Cr stress inhibited the expression of genes related to cell division, and photosynthesis in grain plants while stimulating the expression of genes related to DNA replication and repair, in addition to plant defense systems resist Cr stress. In response to chromium stress, rhizosphere soil bacterial and fungal community compositions and diversity changed significantly (p<0.05). Both bacterial and fungal co-occurrence networks primarily comprised positively correlated edges that would serve to increase community stability. However, bacterial community networks were larger than fungal community networks and were more tightly connected and less modular than fungal networks. The abundances of C/N functional genes exhibited increasing trends with increased Cr exposure. Overall, these results suggest that Cr stress primarily prevented cereal seedlings from completing photosynthesis, cell division, and proliferation while simultaneously triggering plant defense mechanisms to resist the toxic effects of Cr. Soil bacterial and fungal populations exhibited diverse response traits, community-assembly mechanisms, and increased expression of functional genes related to carbon and nitrogen cycling, all of which are likely related to microbial survival during Cr stress. This study provides new insights into resistance mechanisms, microbial community structures, and mechanisms of C/N functional genes responses in cereal plants to heavy metal contaminated agricultural soils. Portions of this text were previously published as part of a preprint (https://www.researchsquare.com/article/rs-2891904/v1).

Comparison of the gut fungal communities among Hooded crane (Grus monacha), Greater white-fronted goose (Anser albifrons), and Bean goose (Anser fabalis) at Shengjin Lake, China

The gut microbes regulate a variety of essential functions in avian hosts. Gut microbes are crucial for understanding avian specie’s ecological role and potential impact on the ecosystem. A wide range of factors shape the gut microbial diversity and communities in avian hosts, including similarity in genotype and shared evolutionary history, particularly in two closely related host species than distinctly related hosts. In this study, high-throughput sequencing methods were applied to compare and study the similarities and differences in the gut fungal communities of two geese from the same genus Anser, Greater white-fronted goose (Anser albifrons, WG), Bean goose (Anser fabalis, BG) with Hooded crane (Grus monacha, HC) sympatric in overlapping niches at Shengjin lake, China. Our findings supported our hypothesis that the two closely related geese shared similar gut fungal alpha diversity patterns compared to Hooded cranes due to similarity in genotype and evolutionary history. In particular, the fungal community composition in the gut of Greater white-fronted goose showed larger variation relative to the other two species. This result suggested that dietary preferences might regulate the gut fungal communities, as Hooded crane and Bean goose share parallel dietary preferences. The results of the abundance null deviation model showed higher values of null deviation (NDV) in Greater white-fronted goose and Bean goose, indicating that the two closely related goose species might be associated with more robust gut filtering for their fungal community relative to Hooded crane species. The fungal co-occurrence networks were complex, with higher stability in the two congeneric geese species relative to Hooded crane. Moreover, 29 animal fungal putative pathogens were identified with high diversity and relative abundance in the two congeneric geese due to their complex migration patterns compared with Hooded cranes. However, due to niche overlap, direct or indirect association may lead to the dissemination of gut microbes among sympatric avian species. These findings have important implications for ecological research, conservation efforts, and wildlife health management. Moreover, these findings illuminate potential ecological and conservation repercussions and increase our understanding of the complex interactions between avian species and their gut flora.

Establishment of Biocontrol Agents and Their Impact on Rhizosphere Microbiome and Induced Grapevine Defenses Are Highly Soil-Dependent

With a reduction in available chemical treatments, there is an increased interest in biological control of grapevine trunk diseases. Few studies have investigated the impact of introducing beneficial microorganisms in the rhizosphere on the existing indigenous soil microbiome. In this study, we explored the effect of two biocontrol agents (BCAs), Trichoderma atroviride SC1 (Ta SC1) (Vintec; Certis Belchim) and Bacillus subtilis PTA-271 (Bs PTA-271), on the grapevine rhizosphere bacterial and fungal microbiome as well as plant defense expression using high-throughput amplicon sequencing and quantitative real-time polymerase chain reaction (PCR), respectively. Additionally, we quantified both Ta SC1 and Bs PTA-271 in the rhizosphere over time using droplet digital PCR. The fungal microbiome was more affected by factors such as soil type, BCA treatment, and sampling time compared with the bacterial microbiome. Specifically, Ta SC1 application produced negative impacts on fungal diversity, whereas application of BCAs did not affect bacterial diversity. Interestingly, the survival and establishment of both BCAs showed opposite trends depending on the soil type, indicating that the physicochemical properties of soils have a role in BCA establishment. Fungal co-occurrence networks were less complex than bacterial networks but highly impacted by Ta SC1 application. Soils treated with Ta SC1 presented more complex and stable co-occurrence networks, with a higher number of positive correlations. Induced grapevine defenses also differed according to the soil, being more affected by BCA inoculation on sandy soil. The findings of this research emphasize the complex relationships among microorganisms in the rhizosphere and highlight the significance of taking into account various factors, such as soil type, sampling time, and BCA treatment, and their influence on the structure and dynamics of microbial communities.

Facilitating Wastewater Purification through Progressive Thawing by Microwave: Responses of Microbial Communities

Freeze–thaw has been proved to be a simple, cost-effective, and highly efficient manner to purify wastewater. However, it remains unclear how microbial compositions and functions in meltwater differentiate over progressive thawing and how such differences affect the end product water quality. In this study, wastewater was frozen, progressively thawed via microwave and collected at five intervals: 5 min, 3 min, 3 min, 3 min, and 3 min (termed as T1~T5). It only took 8 min of microwave and 38.8% of total water to remove more than 75% of the dissolved salt and typical pathogenic microbes, and merely 11 min to reach a removal rate greater than 90%. The Shannon index indicated that the α diversity of bacterial and fungal communities significantly reduced from T1 to T5, and the NMDS dissimilarities also illustrated significantly different β diversity between T1 and T2 and T3, T4, and T5. The OTU-based bacterial and fungal co-occurrence networks developed from T1, T5, and CK were significantly different from each other and clustered in distinct modules. Microbial functional profiles further showed that the meltwater preferentially discharged at T1 selectively removed pathogenic and symbiotic fungi and bacterial subsets associated with endocrine diseases, carbohydrate metabolism, and aging. Yet, other microbial subsets tended to be selectively enriched in the end product at T5, such as saprotrophic fungi and bacterial subsets related to drug resistance, infectious diseases, cancers, and xenobiotics’ biodegradation and metabolism. Overall, the fast thawing facilitated by microwave and in turn the efficient removal of brines from ice crystals offered a new approach to overcome the prolonged time cost required by natural thawing. Selective discharge and enrichment of microbial subsets during progressive thawing alarmingly calls for in-depth investigations on the temporal fluxes of microbes when attempting to reuse wastewater in the regions suitable to apply freeze–thaw protocols.

Native forests transformed into cash crops reduced soil multi-functionality by modifying the microbial community composition and keystone species' abundance in the Jianghuai Hilly Region.

Conversion of native forest to cash crops is the predominant form of land use change in the Jianghuai Hilly Region. However, how plantations with different cash crops affect the soil multi-functionality is not well documented. In this study, we collected three kinds of cash crops soils (vegetable, orchard, and tea) and forest soil, to systematically review the relationship between soil microbial communities and soil multi-functionality. Soil multi-functionality had decreased in vegetable and orchard as compared to native forest, whereas tea plantation had no significant effects on soil multi-functionality. The results also showed that cash crop plantations decreased soil multi-functionality by shifting keystone species' abundance, for forest, vegetable, and orchard, the keystone species that were classified as module hubs in the bacterial co-occurrence network significantly negatively contributed to soil multi-functionality, but the keystone species categorized as module hubs in fungal co-occurrence network positively affected soil multi-functionality. Multiple soil properties were the drivers of the soil microbial community; thus, indicating that the altered soil properties under cash crop plantations were vital in determining microbial composition and biological processes. These results identified that sustainable management strategy in cash crop plantation needed to be developed for improving soil multi-functionality.

Host genetic variation drives the differentiation in the ecological role of the native Miscanthus root-associated microbiome

BackgroundMicrobiome recruitment is influenced by plant host, but how host plant impacts the assembly, functions, and interactions of perennial plant root microbiomes is poorly understood. Here we examined prokaryotic and fungal communities between rhizosphere soils and the root endophytic compartment in two native Miscanthus species (Miscanthus sinensis and Miscanthus floridulus) of Taiwan and further explored the roles of host plant on root-associated microbiomes.ResultsOur results suggest that host plant genetic variation, edaphic factors, and site had effects on the root endophytic and rhizosphere soil microbial community compositions in both Miscanthus sinensis and Miscanthus floridulus, with a greater effect of plant genetic variation observed for the root endophytic communities. Host plant genetic variation also exerted a stronger effect on core prokaryotic communities than on non-core prokaryotic communities in each microhabitat of two Miscanthus species. From rhizosphere soils to root endophytes, prokaryotic co-occurrence network stability increased, but fungal co-occurrence network stability decreased. Furthermore, we found root endophytic microbial communities in two Miscanthus species were more strongly driven by deterministic processes rather than stochastic processes. Root-enriched prokaryotic OTUs belong to Gammaproteobacteria, Alphaproteobacteria, Betaproteobacteria, Sphingobacteriia, and [Saprospirae] both in two Miscanthus species, while prokaryotic taxa enriched in the rhizosphere soil are widely distributed among different phyla.ConclusionsWe provide empirical evidence that host genetic variation plays important roles in root-associated microbiome in Miscanthus. The results of this study have implications for future bioenergy crop management by providing baseline data to inform translational research to harness the plant microbiome to sustainably increase agriculture productivity.7yeh-8ahY_T_UpG1ho_dZsVideo

Restoration Measures of Fencing after Tilling Guided Succession of Grassland Soil Microbial Community Structure to Natural Grassland in the Sanjiangyuan Agro-pasture Ecotone of the Qinghai-Tibetan Plateau.

In the fragile Sanjiangyuan (SJY) agro-pasture ecotone of the Qinghai-Tibetan Plateau (QTP), planting and fencing have been used to alleviate grassland degradation and to provide high-quality grass seeds for the implementation of the project of "grain for green". The soil microbe is the major driving factor in maintaining plant productivity and soil nutrient cycling. However, few studies have explored the effects of planting and fencing on soil microorganisms in the SJY agro-pasture ecotone. We explored the effects of tilling (TG) and fencing after tilling (FTG) on soil microbial communities to reveal the effects of restoration measures on soil microbes and to provide a reference in assessing and improving ecosystem structure. The results showed that restoration measures increased soil microbial species diversity and significantly changed their community structure. We found, the microbial composition was more complex under FTG, and its fungal variability was higher and more similar to that of natural grassland. Additionally, restoration measures resulted in fungal co-occurrence network was more edges, higher density, larger diameter and more positive interactions. This was due to the management of the vegetation-soil microenvironment by FTG inducing a differentiation of microbial community structure. In summary, the implementation of FTG could change the microenvironment in the SJY agro-pasture ecotone, so that variation in the structure of microbial community tended toward that of natural grassland, and increased the stability of microbial co-occurrence network, which was more obvious in the fungal community. HIGHLIGHTS: • Restoration measures have changed the vegetation characteristics and soil microenvironment. • Fencing after tilling (FTG) has brought the microenvironment closer to natural grassland. • FTG significantly increased microbial unique ASVs. The number of fungal unique ASVs was similar to that of natural grassland. • FTG resulted in changes in microbial community structure towards natural grasslands and increased the stability of the microbial co-occurrence network, which was more apparent in the fungal community.