Environmental Microbiome最新文献

Root exudates serve as a bridge connecting plant roots and rhizosphere microbes, playing a key role in influencing the assembly and function of the rhizobiome. Recent studies have fully elucidated the role of root exudates in recruiting rhizosphere microbes to enhance plant performance, particularly in terms of plant resistance to soil-borne pathogens; however, it should be noted that the composition and amount of root exudates are primarily quantitative traits regulated by a large number of genes in plants. As a result, there are knowledge gaps in understanding the contribution of the rhizobiome to soil-borne plant disease resistance and the ternary link of plant genes, root exudates, and disease resistance-associated microbes. Advancements in technologies such as quantitative trait loci (QTL) mapping and genome-wide association studies (GWAS) offer opportunities for the identification of genes associated with quantitative traits. In the present review, we summarize recent studies on the interactions of plant and rhizosphere microbes through root exudates to enhance soil-borne plant disease resistance and also highlight methods for quantifying the contribution of the rhizobiome to plant disease resistance and identifying the genes responsible for recruiting disease resistance-associated microbes through root exudates.

Background: Crop rotation is a sophisticated agricultural practice that can modify the demographic structure and abundance of microorganisms in the soil, stimulate the growth and proliferation of beneficial microorganisms, and inhibit the development of harmful microorganisms. The stability of the rhizosphere microbiome is crucial for maintaining both soil ecosystem vitality and crop prosperity. However, the effects of extended garlic‒maize rotation on the physicochemical characteristics of garlic rhizosphere soil and the stability of its microbiome remain unclear. To investigate this phenomenon, soil samples from the garlic rhizosphere were collected across four different lengths of rotation in a garlic-maize rotation.

Results: There were notable positive associations between the total nitrogen and total phosphorus contents in the soil and the duration of rotation. Prolonged rotation could increase the maintenance of microbiome α diversity. The number of years of rotation and the soil organic carbon (SOC) content emerged as principal determinants impacting the evolution of the bacterial community structure, with the SOC content playing a pivotal role in sculpting the species diversity within the garlic rhizosphere bacterial community. Additionally, SOC remains predominant in shaping the root-associated bacterial community's β-nearest taxon index. However, these factors do not have a notable effect on the fungal community inhabiting the garlic rhizosphere. In comparison with monoculture, rotation can amplify the interconnectivity and intricacy of microbial ecological networks. Long-term rotation can further maintain the stability of both microbial ecological networks and interactions between bacterial and fungal communities. It can enlist a plethora of beneficial Bacillus species microorganisms within the garlic rhizosphere to form a biological barricade that aids in safeguarding garlic against encroachment by the pathogenic fungus Fusarium oxysporum, consequently diminishing disease incidence. This study provides a theoretical foundation for the sustainable development of garlic through long-term crop rotation with maize.

Conclusions: Our research results indicate that long-term garlic‒maize rotation maintains stable garlic rhizosphere microecology. Our study provides compelling evidence for the role of long-term crop rotation in maintaining microbiota and community stability, emphasizing the importance of cultivating specific beneficial microorganisms to enhance rotation strategies for garlic farming, thereby promoting sustainability in agriculture.

Background: Sustainable agriculture increasingly emphasizes the importance of microbial communities in influencing plant health and productivity. In viticulture, understanding the impact of management practices on fungal communities is critical, given their role in disease dynamics, grape and wine quality. This study investigates the effects of integrated, organic, and biodynamic management practices on the diversity and function of fungal communities in a vineyard located in Geisenheim, Germany, focusing on above-ground parts such as bark, leaves, and grapes.

Results: Our findings indicate that while overall fungal species richness did not significantly differ among management systems across various compartments, the composition of these communities was distinctly influenced by the type of management system. In particular, leaf and grape compartments showed notable variations in fungal community structure between integrated and organic/biodynamic management. No differences were observed between organic and biodynamic management. Integrated management demonstrated a significantly higher abundance of mycoparasites in comparison to organic and biodynamic management, primarily attributed to the increased presence of Sporobolomyces roseus, Sporobolomyces ellipsoideus and Rhodotorula glutinis.

Conclusions: The findings highlight the importance of management practices in shaping fungal community composition and function in vineyards. Although overall species richness remained unaffected, community composition and functional diversity varied, highlighting the potential for strategic microbiome management to enhance vineyard sustainability and plant health.

Motivation: Accurate determination and quantification of the taxonomic composition of microbial communities, especially at the species level, is one of the major issues in metagenomics. This is primarily due to the limitations of commonly used 16S rRNA reference databases, which either contain a lot of redundancy or a high percentage of sequences with missing taxonomic information. This may lead to erroneous identifications and, thus, to inaccurate conclusions regarding the ecological role and importance of those microorganisms in the ecosystem.

Results: The current study presents MIMt, a new 16S rRNA database for archaea and bacteria's identification, encompassing 47 001 sequences, all precisely identified at species level. In addition, a MIMt2.0 version was created with only curated sequences from RefSeq Targeted loci with 32 086 sequences. MIMt aims to be updated twice a year to include all newly sequenced species. We evaluated MIMt against Greengenes, RDP, GTDB and SILVA in terms of sequence distribution and taxonomic assignments accuracy. Our results showed that MIMt contains less redundancy, and despite being 20 to 500 times smaller than existing databases, outperforms them in completeness and taxonomic accuracy, enabling more precise assignments at lower taxonomic ranks and thus, significantly improving species-level identification.

Background: The application of a biochar in agronomical soil offers a dual benefit of improving soil quality and sustainable waste recycling. However, utilizing new organic waste sources requires exploring the biochar's production conditions and application parameters. Woodchips (W) and bone-meat residues (BM) after mechanical deboning from a poultry slaughterhouse were subjected to pyrolysis at 300 °C and 500 °C and applied to cambisol and luvisol soils at ratios of 2% and 5% (w/w).

Results: Initially, the impact of these biochar amendments on soil prokaryotes was studied over the course of one year. The influence of biochar variants was further studied on prokaryotes and fungi living in the soil, rhizosphere, and roots of Triticum aestivum L., as well as on soil enzymatic activity. Feedstock type, pyrolysis temperature, application dose, and soil type all played significant roles in shaping both soil and endophytic microbial communities. BM treated at a lower pyrolysis temperature of 300 °C increased the relative abundance of Pseudomonadota while causing a substantial decrease in soil microbial diversity. Conversely, BM prepared at 500 °C favored the growth of microbes known for their involvement in various nutrient cycles. The W biochar, especially when pyrolysed at 500 °C, notably affected microbial communities, particularly in acidic cambisol compared to luvisol. In cambisol, biochar treatments had a significant impact on prokaryotic root endophytes of T. aestivum L. Additionally, variations in prokaryotic community structure of the rhizosphere depended on the increasing distance from the root system (2, 4, and 6 mm). The BM biochar enhanced the activity of acid phosphatase, whereas the W biochar increased the activity of enzymes involved in the carbon cycle (β-glucosidase, β-xylosidase, and β-N-acetylglucosaminidase).

Conclusions: These results collectively suggest, that under appropriate production conditions, biochar can exert a positive influence on soil microorganisms, with their response closely tied to the biochar feedstock composition. Such insights are crucial for optimizing biochar application in agricultural practices to enhance soil health.

Background: Phosphorus (P) plays a vital role in plant growth. The pqqC and phoD genes serve as molecular markers for inorganic and organic P breakdown, respectively. However, the understanding of how P-mobilizing bacteria in soil respond to long-term fertilization and rhizobium application is limited. Herein, soil that had been treated with fertilizer and rhizobium for 10 years was collected to investigate the characteristics of P-mobilizing bacterial communities. Five treatments were included: no fertilization (CK), phosphorus fertilizer (P), urea + potassium fertilizer (NK), NPK, and PK + Bradyrhizobium japonicum 5821 (PK + R).

Results: The soybean nodule dry weight was highest in the P treatment (1.93 g), while the soybean yield peaked in the PK + R treatment (3025.33 kg ha^- 1). The abundance of the pqqC gene increased in the rhizosphere soil at the flowering-podding stage and in the bulk soil at the maturity stage under the P treatment, while its abundance increased in the bulk soil at the flowering-podding stage and in the rhizosphere soil at the maturity stage under the PK + R treatment. The abundance of the phoD gene was enhanced in the bulk soil at the flowering-podding stage under the PK + R treatment. The Shannon and Ace indexes of pqqC- and phoD-harboring bacteria were higher in the rhizosphere soil at maturity under the PK + R treatment compared to other treatments. Furthermore, a comprehensive analysis of the neutral community model and co-occurrence pattern demonstrated that the application of P fertilizer alone led to an increase in the distribution and dynamic movement of pqqC-harboring bacteria, but resulted in a decrease in complexity of network structure. On the other hand, rhizobium inoculation enhanced the distribution and dynamic movement of phoD-harboring bacteria, as well as the stability and complexity of the network structure. Pseudomonas and Nitrobacter, as well as Steptomyces, Stella, and Nonomuraea, may be crucial genera regulating the composition and function of pqqC- and phoD-harboring communities, respectively.

Conclusions: These findings affirm the crucial role of fertilization and rhizobium inoculation in regulating pqqC- and phoD-harboring bacterial communities, and highlight the significance of long-term phosphate-only fertilization and rhizobium inoculation in enhancing dissolved inorganic phosphorus and mineralized organophosphorus, respectively.

Background: An increase in upper-ocean thermal stratification is being observed worldwide due to global warming. However, how ocean stratification affects the vertical profile of plankton communities remains unclear. Understanding this is crucial for assessing the broader implications of ocean stratification. Pelagic ciliates cover multiple functional groups, and thus can serve as a model for studying the vertical distribution and functional strategies of plankton in stratified oceans. We hypothesize that pelagic ciliate communities exhibit vertical stratification caused by shifts in functional strategies, from free-living groups in the photic zone to parasitic groups in deeper waters.

Results: 306 samples from the surface to the abyssopelagic zone were collected from 31 stations in the western Pacific and analyzed with environmental DNA (the V4 region of 18 S rDNA) metabarcoding of pelagic ciliates. We found a distinct vertical stratification of the entire ciliate communities, with a boundary at a depth of 200 m. Significant distance-decay patterns were found in the photic layers of 5 m to the deep chlorophyll maximum and in the 2,000 m, 3000 m and bottom layers, while no significant pattern occurred in the mesopelagic layers of 200 m - 1,000 m. Below 200 m, parasitic Oligohymenophorea and Colpodea became more prevalent. A linear model showed that parasitic taxa were the main groups causing community variation along the water column. With increasing depth below 200 m, the ASV and sequence proportions of parasitic taxa increased. Statistical analyses indicated that water temperature shaped the photic communities, while parasitic taxa had a significant influence on the aphotic communities below 200 m.

Conclusions: This study provides new insights into oceanic vertical distribution, connectivity and stratification from a biological perspective. The observed shift of functional strategies from free-living to parasitic groups at a 200 m transition layer improves our understanding of ocean ecosystems in the context of global warming.

Background: Interactions between plants and diverse root-associated fungi are essential drivers of forest ecosystem dynamics. The symbiosis is potentially dependent on multiple ecological factors/processes such as host/symbiont specificity, background soil microbiome, inter-root dispersal of symbionts, and fungus-fungus interactions within roots. Nonetheless, it has remained a major challenge to reveal the mechanisms by which those multiple factors/processes determine the assembly of root-associated fungal communities. Based on the framework of joint species distribution modeling, we examined 1,615 root-tips samples collected in a cool-temperate forest to reveal how root-associated fungal community structure was collectively formed through filtering by host plants, associations with background soil fungi, spatial autocorrelation, and symbiont-symbiont interactions. In addition, to detect fungi that drive the assembly of the entire root-associated fungal community, we inferred networks of direct fungus-fungus associations by a statistical modeling that could account for implicit environmental effects.

Results: The fine-scale community structure of root-associated fungi were best explained by the statistical model including the four ecological factors/processes. Meanwhile, among partial models, those including background soil fungal community structure and within-root fungus-fungus interactions showed the highest performance. When fine-root distributions were examined, ectomycorrhizal fungi tended to show stronger associations with background soil community structure and spatially autocorrelated patterns than other fungal guilds. In contrast, the distributions of root-endophytic fungi were inferred to depend greatly on fungus-fungus interactions. An additional statistical analysis further suggested that some endophytic fungi, such as Phialocephala and Leptodontidium, were placed at the core positions within the web of direct associations with other root-associated fungi.

Conclusion: By applying emerging statistical frameworks to intensive datasets of root-associated fungal communities, we demonstrated background soil fungal community structure and fungus-fungus associations within roots, as well as filtering by host plants and spatial autocorrelation in ecological processes, could collectively drive the assembly of root-associated fungi. We also found that basic assembly rules could differ between mycorrhizal and endophytic fungi, both of which were major components of forest ecosystems. Consequently, knowledge of how multiple ecological factors/processes differentially drive the assembly of multiple fungal guilds is indispensable for comprehensively understanding the mechanisms by which terrestrial ecosystem dynamics are organized by plant-fungal symbiosis.

With global climate change, ecosystems are affected, some of which are more vulnerable than others, such as alpine ecosystems. Microbes play an important role in environmental change in global ecosystems. Plants and microbes are tightly associated, and symbiotic or commensal microorganisms are crucial for plants to respond to stress, particularly for alpine plants. The current study of alpine and subalpine plant microbiome only stays at the community structure scale, but its ecological function and mechanism to help plants to adapt to the harsh environments have not received enough attention. Therefore, it is essential to systematically understand the structure, functions and mechanisms of the microbial community of alpine and subalpine plants, which will be helpful for the conservation of alpine and subalpine plants using synthetic microbial communities in the future. This review mainly summarizes the research progress of the alpine plant microbiome and its mediating mechanism of plant cold adaptation from the following three perspectives: (1) Microbiome community structure and their unique taxa of alpine and subalpine plants; (2) The role of alpine and subalpine plant microbiome in plant adaptation to cold stress; (3) Mechanisms by which the microbiome of alpine and subalpine plants promotes plant adaptation to low-temperature environments. Finally, we also discussed the future application of high-throughput technologies in the development of microbial communities for alpine and subalpine plants. The existing knowledge could improve our understanding of the important role of microbes in plant adaptation to harsh environments. In addition, perspective further studies on microbes' function confirmation and microbial manipulations in microbiome engineering were also discussed.

Background: Tobacco production faces ongoing challenges due to soil degradation, leading to a persistent decline in yield. Plant growth-promoting fungi (PGPF) have been recognized as an environmentally friendly agricultural strategy. However, many commercial PGPF products exhibit instability due to insufficient environmental compatibility.

Results: In this study, Penicillium sp. PQxj3 was isolated and assessed for its potential to enhance tobacco productivity under field conditions. The results demonstrated that Penicillium sp. PQxj3 treatment significantly promoted the tobacco growth and improved the crop yield. The height of tobacco in Penicillium sp. PQxj3 treatment group significantly increased by 50.19% and 24.05% compared with CK at exuberant and maturity period (P < 0.05). The average yield of tobacco significantly increased by 36.16% compared to CK (P < 0.05). Fungal microbiome analysis revealed that phylogenetically similar probiotic taxa were recruited by Penicillium sp. PQxj3 and reassembled tobacco rhizosphere fungal microbiome. The key chemical indicators of tobacco such as alkaloid, total sugar, and phosphorus were significantly enhanced in Penicillium sp. PQxj3 treatment. The recruited probiotic taxa (Penicillium brasilianum, Penicillium simplicissimum, Penicillium macrosclerotiorum and Penicillium senticosum) were significantly associated with alkaloid, total sugar etc. (P < 0.05), which were identified as the key drivers for improving the chemical components of tobacco. Transcriptome analysis indicated that Penicillium sp. PQxj3 promoted up-regulation of key functional genes involved in alkaloid, indoleacetic, and gibberellin biosynthesis pathways.

Conclusion: In summary, this study assessed the biopromotion mechanism of PGPF Penicillium sp. PQxj3 linking chemical traits, rhizosphere fungal microbiome, and transcriptome profiling. The findings provide a fundamental basis and a sustainable solution for developing fungal fertilizers to enhance agricultural sustainability.