Globally, eutrophication, coastal pollution and thermal stress threaten seagrass ecosystems ecosystems. Consequently, there is a growing need to develop new approaches that work to mitigate these stressors and enhance restoration efforts in seagrass meadows. One promising strategy is to identify, isolate and characterize microbial consortia that are likely to support seagrass productivity. However, our current understanding of key microbial functions that support plant growth in marine systems is limited. Based on evidence from terrestrial plant-microbe systems, seagrass-associated bacteria are expected to provide the plant with nitrogen and phosphorus resources while detoxifying sulfur and producing phytohormones. Here, we sequenced 61 bacterial cultures isolated from the rhizosphere, rhizoplane, and endosphere of the seagrass, Zostera marina to identify a consortium of six putative plant growth promoting (PGP) candidates. Our cultivation approach using plant-based media allowed us to isolate 201 bacteria from Z. marina, including 17 potentially novel species, as well as genera not detected in our amplicon sequencing survey. Genomic and phenotypic analyses of the 61-sequenced pure-cultures revealed that most of the sequenced taxa were able to mobilize nitrogen primarily through catabolic pathways, including denitrification (51
Drought is an increasing threat to soil microbiomes, which underpin critical soil functions and crop production. While drought-induced shifts in soil microbial diversity are well documented, the impact on the functional potential of microbiomes remains poorly understood. It is particularly unclear whether alternative cropping systems, such as organic farming, enhance the ability of microbes to maintain their functionality under drought compared to conventional systems. To fill this gap, we imposed a field-scale drought in a 44-year long-term trial comparing organic and conventional systems, and assessed the functional potential of the wheat rhizosphere microbiome using shotgun metagenomics. Agricultural management legacy was the primary driver of the rhizosphere functional gene composition, accounting for 24–32
Fungicides are widely used to control Fusarium head blight in cereals, yet their effects on mycotoxin contamination remain inconsistent and poorly understood. Here, we combined ITS-based fungal community profiling, targeted Luminex assays for selected Fusarium markers and biosynthetic gene, and quantitative measurement of 47 mycotoxins across two wheat field trials employing distinct fungicide programmes. We examined how chemical disease control reshapes wheat-ear mycobiomes and multi-toxin outcomes. Fungicide application consistently reduced deoxynivalenol and zearalenone by 2.7–4.4-fold but simultaneously increased the sum of T-2 and HT-2 by approximately 3-fold and elevated emerging metabolites, including enniatins and beauvericin. Multivariate ordination revealed clear treatment-associated shifts in mycobiome composition at both sites, with fungicide explaining a measurable proportion of community variation (PERMANOVA (R^2 = 0.078–0.092), (P = 0.001)). Fungicide treatment was also associated with reassembly of conservative Fusarium ITS lineages. Targeted assays showed lower F. graminearum signals in treated plots at both sites, alongside site-specific and more variable responses for other targeted markers. At the community level, fungicide treatment altered trophic composition towards pathotroph-assigned taxa and increased the number of inferred co-occurrence associations. When benchmarked against the current European Union maximum level for unprocessed wheat grain, exceedance of the 50 µg kg⁻¹ limit for the sum of T-2 and HT-2 occurred more frequently in treated plots. Together, these results show that fungicide programmes do not simply suppress mycotoxin risk but can redistribute it through fungal-community restructuring, generating reproducible toxin trade-offs with implications for food-safety surveillance, regulation, and cereal disease management.
Understanding the mechanisms underlying marine fungal community turnover is critical to predicting community responses to climate disturbances. Yet, the interannual stability of mycoplankton community composition, structure, and network organization in the Yellow Sea (YS) remains poorly understood. Here, we investigated fungal community interannual dynamics from 2017 to 2022 within the Yellow Sea Cold Water Mass (YSCWM) and adjacent surface waters in northern (NYS) and southern (SYS) YS during summer. Seawater samples from different depths of the three regions (YSCWM, NYS, and SYS) of the YS were analyzed based on fungal ITS2 amplicon sequencing. Community composition and structure were highly sensitive to environmental disturbances, with sharp declines in diversity and network connectivity. Notably, the record-breaking marine heatwave (2018), local cyclones (2020), and typhoon Lekima (2019) likely decimated dominant fungal taxa and significantly decreased diversity. This environmental fluctuation period coincided with the proliferation of Aspergillus, Alternaria, Cladosporium, Rhodotorula, Acremonium, Malassezia, and Fusarium. Dispersal limitation and drift were the main driving processes of community turnover, with temperature and phosphate as key drivers within the YSCWM and outside at SYS. An increase in seawater temperature and phosphate concentration might lead to a significant decline in fungal diversity. The YSCWM emerged as a critical reservoir of fungal biodiversity, particularly minor taxa that appear to persist under stress. Our findings shed light on the temporal dynamics of fungal communities in the YS, underscoring their susceptibility to drastic oceanic events. Moreover, they highlight the potential role of the YSCWM in ecosystem sustainability under changing climate conditions.
Bamboo forests provide critical ecological and economic benefits in subtropical regions, yet their productivity is often limited by nitrogen (N) availability. Intensive management can significantly increase bamboo productivity, but its impact on the sustainability of soil N cycling remains unclear. This study used metagenomic sequencing to investigate alterations in microbial N cycling across Moso bamboo plantations under contrasting management intensities: intensive (M2), extensive (M1), and unmanaged conditions (M0). Both acid-hydrolyzable N (AHN) and non-AHN were significantly higher (p ≤ 0.05) in M0 than in M1 and M2, whereas amino acid N, ammonia N, and amino sugar N levels declined (p ≤ 0.05) as management intensity increased. Concomitantly, the microbial functional genes shifted from a balanced N-cycling profile in M0 to a denitrification-dominated regime in M2. Specifically, M2 showed suppressed gene abundance for N fixation (nifH) and nitrification (amoC) but a marked increase in denitrification genes (narG, nirK, and nosZ). This transition was mediated by distinct microbial communities: M0 was associated with oligotrophic Chloroflexi, M1 with versatile Proteobacteria and Nitrospirae, and M2 with disturbance-adapted Actinobacteria. Distance-based redundancy analysis and Mantel tests confirmed that soil N fractions were significantly (p ≤ 0.05) correlated with total organic carbon, total phosphorus (P), available P, N-cycling genes, and associated microbial communities. Partial least squares path analysis identified soil P availability as the strongest driver of soil organic N dynamics, highlighting tight N–P coupling. These findings demonstrate that intensive bamboo management shifts the microbial N cycle toward denitrification, converting soil organic N from a conserved pool into a more loss-prone state, with soil P availability as the primary driver. Maintaining long-term soil fertility in bamboo plantations therefore necessitates integrated N-P management strategies.
