ISME communications最新文献

Deep-sea sediments represent a vast yet underexplored reservoir of microbial carbon fixation, playing a critical role in global carbon cycling. However, the vertical distribution of carbon-fixing microorganisms, metabolic pathways, and the underlying energy sources and environmental drivers remain poorly understood. In this study, we investigated microbial carbon fixation and associated energy metabolism in South China Sea (SCS) sediment across 0-690 cm depth. Our findings revealed that dissolved inorganic carbon (DIC) and ammonium (NH₄⁺) concentrations were key environmental drivers of carbon fixation and linked redox processes. Carbon fixation gene diversity increased with sediment depth, while the network complexity of functional genes and taxa involved in these processes declined. A distinct vertical succession of dominant microbial carbon-fixation pathways and their associated energy metabolisms was observed along the sediment depth: the Calvin-Benson-Bassham (CBB) and reductive glycine (rGLY) pathways dominated surface sediments, driven by nitrite oxidation, whereas the Wood-Ljungdahl (WL) pathway prevailed in deeper anoxic layers, supported by hydrogen and carbon monoxide oxidation. Taxonomically, Gammaproteobacteria and Methylomirabilia were abundant carbon-fixing groups in surface sediments, while Desulfobacterota, Chloroflexota, and Aerophobota became predominant at depth. Most carbon-fixing metagenome-assembled genomes (MAGs) exhibited mixotrophic lifestyles, and representative carbon fixation MAGs from Methylomirabilota, Dehalococcoidia (Chloroflexota) and Aerophobetes exhibited different metabolic features compared to their counterparts from other environments. These findings underscore the carbon fixation potential of deep-sea subsurface microbial communities and advance the understanding of carbon fluxes in deep biosphere.

Tourism-driven human activity is increasingly disrupting fragile and once-pristine ecosystems worldwide, as evidenced by coral reef degradation in the Great Barrier Reef, vegetation loss in the Himalayas, and, as demonstrated in this study, microbial shifts in isolated highland habitats such as tepui summits. Integrating field-based ecological, microbiological, and conservation perspectives, this study provides novel insights into how anthropogenic disturbance-particularly tourism-affects microbial functional diversity across interconnected environmental (soil) and host-associated (amphibian skin and faeces) compartments in a globally unique and poorly studied highland ecosystem, the summit of Roraima-tepui in Venezuela. Our results provide clear evidence that anthropogenic disturbance on the summit of Roraima-tepui reduces microbial functional diversity-by 59% in soil and by 21% and 14% in the skin and faecal microbiomes of the (near)endemic toad Oreophrynella quelchii, respectively-compared to pristine sites. Our findings raise significant concern, as alterations in microbial composition and functions could disrupt host immunity and disease resistance in this unique, insular, and ecologically fragile ecosystem, particularly given the recent detection of anthropogenic pathogen incursion in amphibian communities. Our results stress the need to better understand the link between the observed shift in the skin microbiome's functional profiles in O. quelchii at summit sites most impacted by tourism and the recent emergence of the fungal pathogen Batrachochytrium dendrobatidis in the same environmental context. Our findings underscore the urgent need to mitigate human-induced pressures threatening the ecological integrity of the summit of Roraima-tepui, one of the world's most fragile and irreplaceable montane habitats.

Nitric oxide (NO) is a reactive gas that functions as a signaling molecule regulating plant growth and stress responses, while also exerting various roles for microorganisms. In soil, NO is produced through microbial activity, plant metabolism, and physico-chemical processes. However, the impact of exogenous NO on plant physiology and the associated root microbiota remains unexplored. Here, we evaluated the effects of NO exposure on plant physiology, trace gas fluxes and N cycling, as well as the abundance, diversity, and composition of root-associated microbiota. We conducted two 37-day experiments with either Arabidopsis thaliana or tomato (Solanum lycopersicum) plants using innovative plant-soil mesocosms that allowed NO flushing while monitoring the CO₂, N₂O and NO fluxes. The mesocosms were subjected to four NO flushing periods (3-4 days each) at 0 ppbv or 400 ppbv. Our results revealed that exogenous NO₄₀₀ exerted plant-specific effects. While flushing with NO₄₀₀ had no effect on tomato plants or associated microbiota, it increased leaf area in Arabidopsis and modulated the expression of two genes involved in plant growth-defense balance compared to flushing with NO₀. These changes in Arabidopsis physiology were concomitant with modest alterations in the fungal community and a decrease in the abundance of bacterial ammonia-oxidizers, ¹⁵N recovery as NO₃^-, and cumulative CO₂ fluxes. However, it is still unclear how much of these effects were indirectly driven by plant-soil feedbacks. Our findings offer intriguing insights into the possible, though modest, effects of exogenous NO in shaping plant-microbe interactions.

[This corrects the article DOI: 10.1093/ismeco/ycaf156.].

Fecal microbiota transplantation (FMT) is a promising approach for restoring gut microbial balance in both humans and animals. However, the logistical limitations of transplanting fresh fecal samples have increased interest in freeze-dried (lyophilized) fecal material as a transplant inoculum. While lyophilization facilitates storage, it can compromise bacterial viability, which is essential for FMT effectiveness. Lyoprotectants are often used to protect bacterial cultures during freeze-drying, but their effect on complex microbial communities remains unclear, as they may preferentially preserve some taxa over others. This study investigated the impact of four lyoprotectants-mannitol, maltodextrin, trehalose, and a maltodextrin-trehalose mixture-on bacterial viability and community structure in pig fecal samples post-lyophilization. Propidium monoazide (PMA) treatment combined with 16S rRNA sequencing (PMAseq) was used to differentiate viable from non-viable bacteria. In the total community (without PMA), microbial profiles appeared similar across treatment groups. However, when focusing on the viable community (PMA-treated), lyoprotectant choice significantly influenced the post-lyophilization community composition. Gram-negative bacterial viability was especially sensitive to lyophilization. Trehalose and maltodextrin preserved bacterial viability and community structure more effectively than mannitol. Mannitol-treated samples had reduced viable bacterial cells and altered community composition, while trehalose and maltodextrin better maintained diversity and structure of the viable (PMA-treated) communities. Taken together, lyoprotectants have differential effects on microbial composition during lyophilization. Among those tested, trehalose and maltodextrin best preserved both viability and community structure, making them promising candidates for FMT applications. Future research should explore optimizing lyoprotectant formulations to enhance microbiome stability and functional outcomes.

Cold-seep carbonates, formed through interactions among methane, fluid chemistry, and microbial chemosynthesis, represent biodiversity hotspots in the deep sea. Spatial heterogeneity within these carbonates arises from variations in methane flux, yet the microbial contributions to this heterogeneity remain underexplored. Here we combined remotely operated vehicle-based in situ measurements, X-ray imaging, metagenomics, qPCR, and ¹³C-CH₄ stable-isotope labeling to investigate microbial communities across carbonate habitats in the South China Sea. We found that methane flux linked to carbonate structural properties, shapes microbial metabolic interactions, notably anaerobic methane oxidation coupled with aragonite and FeS precipitation. These processes may contribute to self-sealing carbonate features, potentially reducing methane permeability and influencing geochemical gradients and geomorphology. Our findings reveal that microbiomes and their feedbacks play a significant role in shaping habitat-scale spatial heterogeneity of cold-seep carbonates, improving our understanding of methane cycling and carbonate ecosystem dynamics.

As the most abundant marine microorganisms, SAR11 bacteria contribute significantly to global carbon and nutrient cycling. Pelagiphages, viruses that infect SAR11, are potential drivers in structuring the communities, shaping the evolution, and reprogramming the metabolism of SAR11. However, interactions between SAR11 and pelagiphages remain poorly understood. In this study, we investigated and compared the transcriptional dynamics of the SAR11 strain, Candidatus Pelagibacter communis HTCC1062, under independent infection with two phylogenetically distinct pelagiphages: the temperate HTVC019P-type pelagiphage HTVC022P and the lytic HTVC023P-type pelagiphage HTVC027P. These two pelagiphages exhibited distinct infection kinetics, with HTVC022P showing a shorter latent period and a faster host takeover. Transcriptome profiling revealed that infection with HTVC022P and HTVC027P led to the differential expression of 136 and 460 host genes, respectively. Compared to the uninfected control, both pelagiphage infections enhanced host transcription, upregulating the majority of differentially expressed genes. Both pelagiphages induced upregulation of host genes involved in DNA metabolism, transcription, translation, central carbon and nitrogen metabolism. Notably, HTVC027P infection led to the upregulation of 56 genes involved in phosphate, sulfur, and iron metabolism, as well as oxidative phosphorylation and one-carbon metabolism. In contrast, HTVC022P had minimal effects on these pathways. These results suggest that distinct pelagiphages exert unique effects on host metabolic processes, implying divergent ecological implications. Collectively, our study provides new insights into SAR11-pelagiphage interactions, enhancing our understanding of the metabolic states of phage-infected SAR11 bacteria and the ecological functions of phages in marine systems.

The evolutionary adaptation of archaea to ecologically diverse habitats remains poorly understood. Ammonia-oxidizing archaea (AOA) exhibit significant diversification across various environmental conditions; however, their ecological dynamics, diversification, and associated evolutionary processes are still largely unexplored in coastal environments, which contain extensive ecosystem heterogeneity. Combining newly assembled metagenomic data from Chinese marginal seas (2059 km coverage) with global datasets (spanning over 16 000 km), these knowledge gaps were explored across a continental-scale latitudinal gradient. It revealed that coastal AOA genomic diversity is latitude-dependent, with predicted optimum growth temperatures and substrate metabolic pathways explaining the geographical distribution. The two dominant genus-level clades exhibited significantly distinct benthic-pelagic niches, associated with specific genes involved in nutrient uptake and stress resistance. Phylogenomic reconstructions suggest that AOA initially colonized the coastal ocean sediments around 718 million years ago (Mya), and subsequent purifying selection and low recombination facilitated the AOA niche expansion into marine coastal environments. By revealing the evolutionary trajectories of Nitrososphaeria and their differential colonization patterns, our findings offer a novel perspective on the mechanisms of AOA diversification in the coastal ocean. This work advances our understanding of microbial diversification and niche differentiation of AOA in coastal ecosystems as well as the evolutionary forces shaping their global biogeography.

An unbiased and accurate estimation of intraspecies diversity, i.e. the extent of genetic diversity within species (or microdiversity), is crucial for clinical and environmental microbiome studies. Although it is well appreciated that sequencing depth (or coverage depth) below 10X can provide biased estimates of microdiversity, typically underestimating diversity due to the random sampling of alleles, there is a widely accepted convention that microdiversity estimates tend to be relatively stable at sequencing depth exceeding 10X. Therefore, discarding species with <10X or rarefying to 10-20X sequencing depth are generally used to compare microdiversity among taxa and samples. Our findings showed that these biases may persist even at depth levels above 50-200X for all popular sequencing platforms, including Illumina, PacBio, and Oxford Nanopore. The biases mostly, but not always, represent an underestimation of diversity and were attributable to the incomplete recovery of Single Nucleotide Variants (SNVs) at lower sequencing depth levels. To address this issue, we recommend using rarefaction-based approaches to standardize data at least 50X, and ideally at 200X sequencing depth, which reduces differences between observed and expected microdiversity values to <0.5%. Furthermore, the Average Nucleotide Identity of reads (ANIr) metric is significantly less sensitive to sequencing depth variability than nucleotide diversity (π), making it a robust alternative for estimating microdiversity at sequencing depth close or exceeding 10X, without a need to rarefying data. Therefore, the sequencing depth thresholds proposed herein provide a more standardized framework for direct comparisons of microdiversity across samples and studies.

The bacterial-type Wood-Ljungdahl (WL) pathway and reductive tricarboxylic acid (rTCA) cycle are the dominant chemolithotrophic CO₂ fixation pathways in bacteria inhabiting aphotic geothermal and deep-sea hydrothermal ecosystems. However, the activity of these bacterial metabolic systems in ecosystems with available organic carbons remains unclear. Here, we examined the impact of extracellular acetate on the CO₂-fixation pathways of three thermophilic hydrogen-oxidizing and non-acetogenic bacteria using ¹³C tracer-based metabolomics. Under chemolithoautotrophic conditions, Thermodesulfatator indicus and Hydrogenobacter thermophilus fixed CO₂ through the WL pathway and rTCA cycle, respectively, whereas Thermovibrio ammonificans, which has been suggested to operate both of these pathways, exhibited significant CO₂ fixation through only the rTCA cycle. Under chemolithomixotrophic conditions with acetate, H. thermophilus and T. ammonificans assimilated both CO₂ and acetate via the rTCA cycle. In contrast, acetate suppressed CO₂ fixation through the WL pathway in T. indicus and was used as the primary carbon source under chemolithomixotrophic conditions. These results suggest that the contribution of the WL pathway for CO₂ fixation might be overestimated in ecosystems where acetate is available. Moreover, the present findings indicate that simultaneous CO₂ fixation through both the WL pathway and rTCA cycle in a cell, which has been proposed as a possible metabolic strategy for CO₂-fixation in ancestral life, is not advantageous in extant microorganisms.