Sediment depth-related variations of comammox Nitrospira: Evidence in the Three Gorges Reservoir, China.

The recent discovery of comammox Nitrospira as complete ammonia-oxidizing microorganism has fundamentally revolutionized our understanding of nitrogen cycling in sediment environments. However, knowledge regarding their abundance, biodiversity, community structure, and interactions is predominantly limited to the upper layers (0-20 cm). To address this gap, we collected sediment samples along profiles ranging from 0 to 300 cm in depth at three locations within the middle segment of the Three Gorges Reservoir (TGR), China. Quantitative real-time PCR (qPCR) analyses suggested that comammox bacteria were not only ubiquitous in deep sediments but also more abundant than ammonia-oxidizing bacteria (AOB). Ammonia monooxygenases subunit A (amoA) gene amplicon sequencing illuminated that comammox bacteria were more sensitive to sedimental depth compared to AOB and ammonia-oxidizing archaea (AOA), as evidenced by a more significant decline in community diversity and similarity over distance along sediment vertical profiles. Notably, we discovered that the amoA gene abundance, alpha- and beta-diversity of comammox bacteria exerted an essential contribution to potential nitrification rates according to random forest model. Phylogenetic analysis indicted that most comammox bacteria within sediment samples belonged to clade A.2. Intriguingly, the average relative abundance of comammox clade A.2 displayed a noteworthy rise with sediment depth, whereas clade A.1 demonstrated a converse pattern, unveiling distinct ecological niche adaptations of these two clades along the sediment profile. Ecological network analysis further revealed closer interactions between comammox bacteria and canonical ammonia oxidizers in the superficial layer (0-40 cm), with the network structure gradually simplifying from superficial to deep sediment (200-300 cm). Overall, these findings broaden the current recognition of the geographic distribution and niche segregation of comammox bacteria at the fine scale of the sediments ecosystems and provide insights into sediment depth-related variations of their coexistence network patterns in large freshwater reservoirs.

Vertical variation in prokaryotic community composition and co-occurrence patterns in sediments of the Three Gorges Reservoir, China.

Archaea and bacteria are distributed throughout the sediment; however, our understanding of their biodiversity patterns, community composition, and interactions is primarily limited to the surface horizons (0-20 cm). In this research, sediment samples were collected from three vertical sediment profiles (depths of 0-295 cm) in the Three Gorges Reservoir (TGR), one of the largest reservoirs in the world. Through 16S rRNA sequencing, it was shown that sediment microbial diversity did not significantly vary across the sediment. Nevertheless, a decline in the similarity of archaeal and bacterial communities over distance along sediment vertical profiles was noted. Nonmetric multidimensional scaling (NMDS) analysis revealed that archaeal and bacterial communities could be clearly separated into two groups, located in the upper sediments (0-135 cm) and deep sediments (155-295 cm). Meanwhile, at the fine-scale of the vertical section, noteworthy variations were observed in the relative abundance of prominent archaea (e.g., Euryarchaeota) and bacteria (e.g., Proteobacteria). The linear discriminant analysis effect size (LEfSe) demonstrated that twenty-four bacterial and twenty-six archaeal biomarker microbes exist in the upper and deep sediment layers. Each layer exhibited distinctive microbial divisions, suggesting that microbes with diverse biological functions are capable of thriving and propagating along the sediment profile. Co-occurrence network analysis further indicated that the microbial network in the upper sediments was more complex than that in the deep sediments. Additionally, the newly discovered anaerobic methanotrophic archaeon Candidatus Methanoperedens was identified as the most abundant keystone archaeal taxon in both sediment layers, highlighting the significance of methane oxidation in material cycling within the TGR ecosystem. In summary, our study examined the biodiversity and coexistence patterns of benthic microbial communities throughout the vertical sediment profile, providing detailed insights into the vertical geography of archaeal and bacterial communities in typical deep-water reservoir ecosystems.

Plant Triterpenoids Regulate Endophyte Community to Promote Medicinal Plant Schisandra sphenanthera Growth and Metabolites Accumulation.

Beneficial interactions between endophytes and plants are critical for plant growth and metabolite accumulation. Nevertheless, the secondary metabolites controlling the feedback between the host plant and the endophytic microbial community remain elusive in medicinal plants. In this report, we demonstrate that plant-derived triterpenoids predominantly promote the growth of endophytic bacteria and fungi, which in turn promote host plant growth and secondary metabolite productions. From culturable bacterial and fungal microbial strains isolated from the medicinal plant Schisandra sphenanthera, through triterpenoid-mediated screens, we constructed six synthetic communities (SynComs). By using a binary interaction method in plates, we revealed that triterpenoid-promoted bacterial and fungal strains (TPB and TPF) played more positive roles in the microbial community. The functional screening of representative strains suggested that TPB and TPF provide more beneficial abilities to the host. Moreover, pot experiments in a sterilized system further demonstrated that TPB and TPF play important roles in host growth and metabolite accumulation. In summary, these experiments revealed a role of triterpenoids in endophytic microbiome assembly and indicated a strategy for constructing SynComs on the basis of the screening of secondary metabolites, in which bacteria and fungi join forces to promote plant health. These findings may open new avenues towards the breeding of high yielding and high metabolite-accumulating medicinal plants by exploiting their interaction with beneficial endophytes.

Phytoremediation potential of Youngia japonica (L.) DC: a newly discovered cadmium hyperaccumulator.

Cadmium (Cd) is one of the most toxic contaminants, causing a lot of harm to environment and the human health. An outdoor pot experiment for 60 days was conducted to study the Cd(II) effects on growth, biomass, physiological properties, Cd uptake, and accumulation in Youngia japonica plants but also to evaluate the effect of Y. japonica growth on enzyme activity of Cd-contamination soils. Generally, the application of Cd(II) less than 120 mg kg-1 stimulated the growth of the plants, whereas at 160 mg kg-1 or higher levels, a significant reduction was observed. For all treatments > 10 mg kg-1 Cd(II) in soil, values of Cd in roots and aboveground parts were more than the critical value of 100 mg kg-1 and reached highest values of 252.51 and 314.29 mg kg-1, respectively. The bioconcentration factors (BCF) and translation factors (TF) for all Cd treatments were more than 1.0, with the former ranging from 1.03 to 5.46 and the later from 1.04 to 1.33. The activities of peroxidase (POD) and superoxide dismutase (SOD), as well as the levels of glutathione (GSH) and proline in Y. japonica plants after exposure to 10-200 mg kg-1 Cd(II) were stimulated, implying that they were defensive guards to the oxidative stress produced by Cd. The urease, dehydrogenase, and alkaline phosphatase activities under low Cd concentrations can be enhanced by planting Y. japonica species but inhibited under high Cd concentrations. Our data provide comprehensive evidence that Y. japonica has the typical properties of a Cd hyperaccumulator and thus may be practically employed to alleviate Cd from contaminated soils.

Kadanguslactones A-E, further oxygenated terpenoids from Kadsura angustifolia fermented by a symbiotic endophytic fungus, Penicillium ochrochloron SWUKD4.1850.

The fermentation of Kadsura angustifolia with an endophytic fungus, Penicillium ochrochloron SWUKD4.1850 yielded five additional undescribed oxygenated terpenoids, kadanguslactones A-E, together with ten known compounds. Their structures were established by the extensive 1D, 2D-NMR, HR-ESI-MS, CD and X-ray crystallography data analysis. Kadanguslactone A is the first example of 1,30-cyclo-3,4; 9,10-disecocycloartanes that combine a five-membered lactone ring A with a cyclopentane ring B consisting of C-1, C-4, C-5, C-10, C-30. Kadanguslactone B was a rare highly oxygenated 18-norschiartane-type bisnortriterpenoid with spirocyclis rings F and G, whereas kadanguslactone C was an uncommon henrischinin-type schitriterpenoid containing a unique 3-one-2-oxabicyclo [3,2,1]-octane motif. The cytotoxicity against HepG2 cell line of all compounds were evaluated. Except nigranoic acid, all other metabolites have been first found in unfermented K. angustifolia, suggesting that main functional ingredients from K. angustifolia may be converted by P. ochrochloron SWUKD4.1850 into highly oxygenated terpenoids. This study provided a fascinating prospective for setting up alternative processing techniques to enhance the functionality and utility of Chinese herbal medicine.

Diversity and bioactivities of fungal endophytes from Distylium chinense, a rare waterlogging tolerant plant endemic to the Three Gorges Reservoir.

BACKGROUND: The present study involves diversity and biological activities of the endophytic fungal community from Distylium chinense, a rare waterlogging tolerant plant endemic to the Three Gorges Reservoir. This study has been conducted hypothesizing that the microbial communities in the TGR area would contribute to the host plant tolerating a range of abiotic stress such as summer flooding, infertility, drought, salinity and soil erosion etc., and they may produce new metabolites, which may possess plentiful bioactive property, especially antioxidant activity. Therefore in the current study, the antioxidant, antimicrobial and anticancer activities of 154 endophytes recovered from D. chinense have been investigated. Furthermore, the active metabolites of the most broad-spectrum bioactive strain have also been studied. RESULTS: A total of 154 fungal endophytes were isolated from roots and stems. They were categorized into 30 morphotypes based on cultural characteristics and were affiliated with 27 different taxa. Among these, the most abundant fungal orders included Diaporthales (34.4%) and Botryosphaeriales (30.5%), which were predominantly represented by the species Phomopsis sp. (24.7%) and Neofusicoccum parvum (23.4%). Fermentation extracts were evaluated, screening for antioxidant, antimicrobial and anticancer activities. Among the 154 isolates tested, 99 (64.3%) displayed significant antioxidant activity, 153 (99.4%) exhibited inclusive antimicrobial activity against at least one tested microorganism and 27 (17.5%) showed exclusive anticancer activity against one or more cancer cell lines. Specifically, the crude extract of Irpex lacteus DR10-1 exhibited note-worthy bioactivities. Further chemical investigation on DR10-1 strain resulted in the isolation and identification of two known bioactive metabolites, indole-3-carboxylic acid (1) and indole-3-carboxaldehyde (2), indicating their potential roles in plant growth promotion and human medicinal value. CONCLUSION: These results indicated that diverse endophytic fungal population inhabits D. chinense. One of the fungal isolate DR10-1 (Irpex lacteus) exhibited significant antioxidant, antimicrobial and anticancer potential. Further, its active secondary metabolites 1 and 2 also showed antioxidant, antimicrobial and anticancer potential.