Environmental Microbiome最新文献

Background: Anaerobic digestion (AD) offers a cost-effective and efficient approach for wastewater treatment, but the mesophilic anaerobic digestion only well performed within a narrow temperature range, typically between 30 and 40 °C. However, lower temperatures affected the performance of AD, microbial community and granular sludge properties. Recent studies mainly focused on adding exogenous quorum sensing (QS) signal molecules to accelerate the recovery of anaerobic digestion performance under pressure conditions, while few studies on endogenous QS molecules. To investigate microbial stress adaptation mediated by endogenous QS system under stepwise temperature reduction, an Upflow Anaerobic Sludge Blanket (UASB) reactor with gradual temperature reduction from 35 to 20 °C was constructed.

Results: This study investigated the performance and microbial dynamics of the UASB reactor subjected to gradual temperature reduction from 35 to 20 °C. The reactor maintained stable COD removal efficiency (78-79%) even at 20 °C after adaptation. Temperature reduction shifted microbial community structure, with Proteobacteria becoming dominant at lower temperatures. Especially, Pleomorphomonas and the Christensenellaceae R-7 group are highly adaptable to low temperatures, and their flourish was the microbial basis of sustained performance of UASB under low-temperature stress. In archaeal community, the relative abundance of Methanosaeta belong to acetoclastic methanogen decreased, while the hydrogenotrophic methanogens Methanobacterium and Methanospirillum increased. These findings indicated that the methanogenic pathway transitioned from acetoclastic to hydrogenotrophic, likely contributing to sustained methanogenic activity. The results of Mantel test between QS molecules profiles, microbial community and granular sludge properties revealed the endogenously generated AHLs and AI-2 play a crucial role in optimizing the bacterial and methanogenic communities, resulting in faster recovery of the anaerobic sludge from temperature reduction.

Conclusions: Quorum sensing molecules, especially AHLs and AI-2, played a crucial role in regulating microbial social behaviors and EPS production under temperature stress. Moreover, These QS changes coincide with a shift from acetoclastic to hydrogenotrophic methanogenesis and with EPS composition adjustments (PN/PS changes), suggesting that QS promotes low-temperature adaptation by regulating EPS secretion and community adhesion, thereby stabilizing granule structure and maintaining metabolic syntrophy and methanogenesis. These findings enhance our understanding of temperature effects on anaerobic systems and provide a basis for optimizing psychrophilic anaerobic processes, addressing the need for energy-efficient wastewater treatment in colder climates.

Herbarium specimens are invaluable for studying plant. Yet their potential to reveal historical plant-associated microbiomes remains largely unexplored. To address this gap, we reconstructed the temporal and spatial dynamics of foliar fungal endophytes in Norway spruce (Picea abies) by sequencing the fungal internal transcribed spacer (ITS) region from herbarium needle specimens collected in Finland between 1861 and 2023. We analyzed community shifts across 50-year and 20-year intervals and between southern and northern regions, assessing the influence of temperature and precipitation. The results showed that the community was dominated by Ascomycota, with Lophodermium, Ceratocystis, Yarrowia, Saccharomyces, and basidiomycete Heterobasidion as the most abundant genera. Among the 50-year intervals, H. parviporum was detected, and the abundance of Lophodermium picea increased in 20-year interval (2001-2023, P < 0.05). The fungal community composition differed significantly between the interval 1951-2000 and both 1851-1900 and 1901-1950 (P < 0.05). The southern region exhibited distinct fungal community and lower alpha diversity indices compared to the north (P < 0.05). Functional prediction revealed that pathogen relevant traits and saprotroph relevant traits were dominant modes across the samples. While temporal and spatial factors significantly structured the communities, no direct correlation with historical temperature or precipitation was found. Our findings demonstrate that herbarium specimens are a powerful resource for uncovering long-term microbial dynamics and highlight the primary roles of time and geography in shaping the foliar mycobiome.

Background: Soil microbiota are key players of terrestrial ecosystem functioning, including decomposition, soil organic matter formation, and nutrient cycling, and interact strongly with plants in the rhizosphere. Several studies have demonstrated the potential of plants to alter soil microbiome assembly and functioning (i.e., through manipulation of soil organic matter pools via root exudation), which can be critical for sustaining soil ecosystem functioning. Using soil from a long-term biodiversity experiment in Germany, we investigated how soil microbial communities responded to variations in plant species richness (1-16 species), functional group richness (1-4 groups), and plant identity (grasses, legumes, small herbs, and tall herbs) using 16S rRNA gene and ITS amplicon sequencing. We examined bacterial and fungal community structure, metabolic potential, and microbial network architecture to better understand the role of the soil microbiome and its net positive relationship between biodiversity and ecosystem functioning.

Results: Plant diversity induced gradual shifts in microbial community composition, while increasing soil organic carbon and nitrogen stocks. Microbial networks exhibited increased connectivity, particularly between bacteria and fungi. Meanwhile, mutualistic and antagonistic functional guild representation increased, that is the sum total of plant-beneficial (i.e., endophytes) and plant- or fungi-detrimental (i.e., pathogens and parasites) fungal guilds, respectively. Key nodes shifted from generalist taxa at low plant diversity to more specialized communities at high plant diversity. Notably, fungi responded more strongly than bacteria, and their functional potential was driven by plant functional identity rather than species richness.

Conclusion: At low plant diversity, generalist taxa likely exploit less complex and diverse organic carbon inputs, allowing them to dominate available niches. In contrast, higher plant diversity promotes a broader array of specialist taxa that likely benefit from the greater diversity of organic carbon compounds, and thus greater niche availability. As network complexity grows, ecosystem functions are being distributed across more taxa, leading to greater microbiome stability, and ultimately more efficient soil carbon and nutrient cycling. Our findings suggest that higher plant diversity strengthens microbial functioning and enhances microbiome resilience, that is the capacity of the microbial community to maintain soil functioning despite environmental disturbances.

Background: Fungal communities play crucial roles in plant development and metabolite accumulation, especially in fully mycoheterotrophic medicinal plants like Gastrodia elata. While the importance of fungal symbiosis in G. elata is recognized, how fungal community dynamics evolve across its entire growth cycle and how they influence biomass and bioactive compound accumulation remain largely unclear.

Results: High-throughput sequencing combined with multi-omics analyses revealed that developmental progression significantly shapes fungal diversity and composition, thereby influencing biomass and metabolite accumulation in G. elata. These effects are mediated by stage-specific selective recruitment and dynamic remodeling of fungal communities in both rhizome and rhizosphere compartments. Structural equation modeling indicated that developmental stage, fungal α-diversity, and community structure exert both direct and indirect effects on biomass and the accumulation of bioactive compounds. High-resolution association network analyses further identified key functional fungal groups, particularly wood and soil saprotrophs, as major contributors to seed stem biomass regulation. Notably, the symbiotic fungus Armillaria showed the strongest positive correlation with gastrodin accumulation, while wood saprotrophs and plant pathogens also significantly influenced its levels.

Conclusions: This study systematically elucidates the dynamic changes in fungal communities across different developmental stages of G. elata and their effects on biomass and bioactive metabolite accumulation. Our findings highlight the central role of microbe-plant-metabolite interactions in regulating biomass and bioactive metabolite production, offering valuable insight for optimizing the cultivation and quality of medicinal plants through microbiome-targeted strategies.

Background: Trees and their associated microbes provide numerous ecosystem services including carbon sequestration, nutrient cycling and phytoremediation. Tree bark represents a large and seasonably stable habitat for microbial communities. However, the tree bark microbiome remains largely understudied, particularly for wetland tree species. In the Lower Mississippi River Basin, bald cypress (Taxodium distichum) are the predominant tree species in many wetlands, including lakes and streams connected to large agroecosystems dominated by row-crop agriculture. These water bodies are often managed for irrigation and drainage needs and are subject to agrochemical runoff from adjacent fields. Thus, we sought to understand how hydrology affects the bald cypress bark microbiome.

Results: We collected 278 bark samples over six months from 18 trees located in three different lakes. Using 16S rRNA gene sequencing, we found that the bald cypress tree bark microbiome was largely consistent between trees within a lake as well as between different lakes, with a core microbiome that includes bacterial taxa that were present in over 95% of samples collected. Hydrology had a significant influence on microbiome structure, with different sections of bark having distinct bacterial communities depending on if the bark was submerged, just above the water, or dry. Water quality was significantly correlated with alpha diversity of wet bark, which was more diverse than dry bark and had higher relative abundances of bacteria that may be providing relevant ecosystem services such as denitrification, methane oxidation, and pollutant degradation.

Conclusions: Wetlands are important for nutrient cycling and water quality regulation. Our study provides insights into microbial dynamics of these ecosystems and how hydrology can impact the microbial communities present, which in turn may be impacting water quality. This work is the first to the describe the bark microbiome of a wetland tree species and lays the groundwork for future studies assessing the functional role of the microbiome in wetland ecosystem services.

Lettuce, a widely consumed raw vegetable, harbors leaf-associated microbial communities whose understanding and prediction are crucial for plant and human health. While environmental factors are known to strongly influence plant leaf microbiomes, the role of plant-specific determinants in shaping microbial diversity remains unclear. In this study, we investigated how three key plant factors -genetic distance, plant variety and leaf micro- and macronutrient content- influence the composition and diversity of lettuce leaf bacterial communities, by analyzing 131 fully-sequenced Lactuca sativa genotypes via 16S rRNA amplicon sequencing. Our findings revealed that variety, as defined by breeders, exerts a greater influence on bacterial community diversity than genetic distance or variations in leaf nutrient levels. Together with available and detailed shoot traits they explained 13.4% of the observed bacterial diversity. Inspection of 9 specific leaf morphological traits, with further validation by MAGs analysis, showed that heart formation, head height, and venation types significantly shaped bacterial richness and evenness, mainly acting on non-hub members. These results highlight the strong relationship between leaf morphology and bacterial community structure, suggesting that phenotypic traits play an outsized but understudied role in shaping the leaf microbiota, a crucial aspect of the edible microbiome.

Introduction: The impacts of incorporating legumes into cereal crops on soil microbial structure, composition, functional genes involved in nitrogen, carbon and phosphorus cycling, signaling pathways and hydraulic conductivity adaptations have been well studied. However, the same cannot be said for functional genes that increase drought tolerance.

Objectives: Here, we examined the changes in microbial community structure and functional genes involved in drought tolerance in response to legume‒cereal rotation and cereal‒cereal rotation. This study provides a preliminary, exploratory characterization of microbial community and functional gene shifts, without direct evidence of functional impact on plant physiology or productivity.

Methods: DNA extracted from soil samples collected across cowpea-sorghum treatment (CS) or maize-sorghum treatment (MS) was sequenced via shotgun sequencing.

Results: Nonmetric multidimensional scaling analysis revealed that the microbial communities in the CS treatment significantly differed from those in the MS treatment. Compared with the MS rotation, the CS rotation increased the relative abundances of Pseudomonadota, Acidobacteriota, Chloroflexota, Gemmatimonadota, Euryarchaeota, and Candidatus Bathyarchaeota and reduced the abundances of Actinomycetota, Ascomycota, and Nitrososphaerota at the phylum level. Furthermore, the CS rotation increased the abundance of microbial genera such as Solirubrobacter, Sphingomonas, Nitrosocosmicus, Nitrosotenuis Aspergillus, and Metschnikowia when related to the MS rotation. STAMP analysis revealed that in the CS rotation, genes involved in trehalose biosynthesis, biofilm formation, oxidative stress mitigation (e.g., sodA, katG), stress signaling (e.g., rpoS, ipdC), nutrient provisioning (e.g., nifH, pqqC), membrane fluidity (desA, desB), dormancy (spo0A, spoVF), and ion homeostasis (nhaB, kup) predominated. In the MS rotation, proline biosynthesis (proA, proB, and proC), glycine betaine synthesis (betA and betB), aquaporin (aqpZ), and structural integrity genes (murA and murC) were predominant. The RDA results revealed that crop rotation influenced the soil physicochemical parameters, which in turn impacted both the microbial communities and drought tolerance genes in both treatments, probably creating a favorable environment for resilience under drought.

Conclusion: These research findings provide insight into the relationships between cowpea cropping sequences and the soil microbiome and drought-tolerant functional genes fundamental for the productivity of successive crops and this understanding guides sustainable crop selection.

Background: Soil denitrification mediated by microbial communities is a major source of nitrous oxide (N₂O), a potent greenhouse gas. However, the regulatory roles of keystone taxa in this process remain poorly understood, particularly under distinct edaphic conditions. Black soil (BS) and fluvo-aquic soil (FS), two representative agricultural soils in China, exhibit contrasting N₂O emission potentials, offering an ideal model for exploring microbial mechanisms driving soil-specific denitrification dynamics.

Results: We integrated microbial co-occurrence networks, metagenomics, and functional phenotyping to identify and characterize keystone bacterial taxa involved in denitrification across the two soil types. Structural equation modeling (SEM) and correlation analyses revealed strong associations between keystone taxa and denitrification rates and N₂O emission patterns. Ensifer ASV205 was identified as a conserved keystone taxon in both soils and exhibited strain-level niche specialization. Comparative genomic analysis revealed that variations in denitrification gene composition and carbon-nitrogen metabolic pathways enabled Ensifer strains to act either as N₂O producers or reducers, depending on environmental conditions.

Conclusions: Our findings demonstrate that soil-specific denitrification processes and N₂O emissions are governed by keystone taxa through adaptive genomic and metabolic strategies shaped by environmental filtering. This study provides new insights into the microbial mechanisms regulating N₂O emissions and lays the groundwork for developing microbiome-informed strategies to mitigate greenhouse gas emissions in agricultural soils.

Background: Karst rocky desertification poses a serious threat to the ecosystems of southwest China, where Hypnum leptothallum plays a crucial role in forming microbial crusts essential for restoration. However, the use of native microbial applications in this area remains largely unexplored.

Results: In this study, the host-associated microbial communities of H. leptothallum from four severely desertified regions in Guizhou Province were characterized using high-throughput sequencing. The results revealed conserved α- and β-diversity, with dominant bacterial phyla being Pseudomonadota (34-47%) and Actinomycetota (23-35%), and fungal phyla being Ascomycota (57-83%) and Basidiomycota (14-32%). Subsequent carbon-source preference analysis guided the formulation of specialized media (e.g., α-D-lactose, N-acetyl-D-glucosamine) to isolate culturable strains, with cross-referencing identifying 14 bacterial and 36 fungal species consistently shared between sequencing and cultivation. Functional evaluation demonstrated bacterial dominance in inorganic phosphorus solubilization (68% of strains), protease synthesis (76%), ammonia production (56%), and indole-3-acetic acid biosynthesis (62%), while fungi excelled in organophosphorus solubilization. Further drought tolerance and gametophyte co-culture assays identified 10 drought-resistant bacterial strains and 16 strains significantly enhancing H. leptothallum growth within 7 days.

Conclusions: These functionally validated strains, particularly drought-adapted and growth-stimulating species closely related to Rhodococcus erythropolis, provide targeted microbial resources for developing synthetic inoculants to optimize artificial crust propagation in karst restoration.

Background: The Barrancas Blancas (BB) plain, situated in the high-altitude Atacama region, is a cryogenic, hyper-arid, poly-extreme environment. The seasonal formation of a temporary freshwater lake under these harsh conditions provides a unique opportunity to examine how liquid water influences the metabolic responses of desert microbial communities. Using a metatranscriptomic approach, we characterised microbial community responses along a 70-meter natural moisture gradient.

Results: Along the gradient, the most active sites (8-23 m from the lake) exhibited high RNA recovery and diverse metabolic functions. Bacillariophyta (diatoms) drove oxygenic phototrophy, while Pseudomonadota contributed to anoxygenic phototrophy and nitrogen fixation. Additionally, Pseudomonadota, Actinomycetota, and Bacteroidota expressed genes for the oxidation of nitrate, sulfide, thiosulfate, and trace gases (H₂, CO). The energy derived from these processes was reflected in the high capacity for carbon fixation by these taxa. Moreover, network analysis revealed that these primary producers co-occurred with a diverse range of heterotrophic prokaryotic and eukaryotic groups. In contrast, at the driest site, hydrogen oxidation was the primary energy-conserving process, predominantly associated with Actinomycetota, which also contributed to hydrogenotrophic carbon fixation. Notably, even at this site, heterotrophic eukaryotes co-occurred with these chemolithotrophic primary producers.

Conclusions: This study presents the first transcriptomic analysis from the high-altitude Atacama Desert, facilitated by the favourable moisture conditions. Furthermore, these findings highlight a moisture-driven transition in microbial energy acquisition strategies and emphasise the ecological significance of both photoautotrophy and chemolithotrophy, which likely vary depending on the dynamics of temporary lakes. The BB plain and its lake thus offer a robust model for understanding microbial resilience, functional plasticity, community assembly, and trophic interactions in extreme environments, providing novel insights into life at the edge of habitability.