ISME communications最新文献

Primary production in aquatic systems is governed by interactions between microalgae and their associated bacteria. Most of our knowledge about algal microbiomes stems from natural mixed communities or isolated algal monocultures, which therefore does neither address the role of genotypic diversity among the algal host cells nor do they reveal how this host diversity impacts the assembly process of associated bacteria. To overcome this knowledge gap, we developed a single-cell 16S sequencing approach in combination with CRISPR-Cas9 guided depletion of host 16S contaminations from the chloroplast. The validity of this novel method was tested by comparing bacterial communities of 144 single-cells across three genotypes of the Arctic marine diatom Thalassiosira gravida grown under different environmental conditions. From these, 62 single-cells were additionally sequenced after CRISPR-Cas9 treatment. Due to the improved sequencing depth, bacterial richness associated with individual diatom cells was increased by up to 56%. By applying this CRISPR-Cas9 treatment we not only revealed intraspecific host-genotype associations but also low-abundance bacterial taxa that were not detected by standard 16S rRNA gene metabarcoding. Thus, the CRISPR-Cas9 assisted single-cell approach developed in this study advances our understanding on how the intraspecific diversity among algal hosts impacts the assembly process of their associated bacteria. This knowledge is essential to understand the co-evolution and adaptation of species in algal microbiomes.

Diazotrophy is the most important nitrogen source in the oligotrophic surface ocean, but the organisms involved and their contributions are incompletely understood due to limited observations. Only diazotrophic organisms possess the nifH gene to reduce dinitrogen to ammonium, but their distribution and activity can only be quantified through sampling and experiments during research cruises. Some recent studies document small diatoms with symbionts able to fix nitrogen, a new source of biologically available nitrogen in addition to the well-known cyanobacterial species such as Trichodesmium or symbionts of haptophytes (UCYN-A) and diatoms (Diatom-Diazotroph Associations, or DDAs). Here, we document a very active symbiosis between small pennate diatoms such as Mastogloia and Haslea with rhizobial and cyanobacterial symbionts in waters of the Western tropical North Atlantic influenced by the Amazon River plume. We used NanoSIMS analysis of ¹⁵N₂ tracer experiments to quantify high rates of nitrogen fixation in generally abundant, symbiont-bearing pennate diatoms. This newly described symbiosis may contribute a previously unquantified flux of biologically available nitrogen to oceanic systems. Pennate diatoms and their symbionts may close a key gap in our understanding of the supply of nutrients to the ocean and provide a previously unknown biological sink for carbon dioxide.

Ocean acidification (OA) and ocean warming (OW) pose escalating threats to marine ecosystems, particularly to benthic organisms, such as sea cucumbers, that play pivotal roles in nutrient cycling and sediment health. Existing research mainly addresses sea cucumbers' physiological responses, overlooking gut microbial communities and metabolites in their stress adaptation. Herein, a mesocosm was constructed and analyzed by using integrated gut microbiome and metabolomics approaches to investigate the responses of sea cucumbers Apostichopus japonicus to OA and OW. Results revealed that microbial community plasticity underpins holobiont adaptation, with warming restructuring gut microbiota toward thermotolerant taxa, whereas acidification enriches alkalinity-modulating Rhodobacteraceae and Halioglobus sp. Metabolomic profiling identified 43 amino acid derivatives with significantly increased concentrations in OA and OW groups, including upregulated N-methyl-aspartic acid and γ-glutamyl peptides that stabilize macromolecules and enhance redox homeostasis. Conversely, antioxidative metabolites (e.g., ergothioneine, L-homocystine) are suppressed, reflecting trade-offs between energy allocation and stress protection. In OW group, the antioxidant synthesis pathway is shifted to energy metabolism related to heat tolerance, whereas in OA group, energy is preferentially used for alkalinity regulation pathways rather than oxidative stress defense. Changes in microbial community structure mechanistically explain the trends in metabolite concentrations, as the proliferation of Vibrio spp. in the OW group drives lysine catabolism, leading to a significant increase in L-saccharopine levels. Bacteroidetes reduction in the OA group correlates with L-homocystine downregulation, suggesting that pH-driven microbial interactions are disrupted. These findings demonstrate gut microbiota reshape community structure and metabolism to mitigate synergistic climate stress, emphasizing microbiome-mediated resilience in marine ecosystems amid global climate change.

Marine sediment contains some of the most abundant and diverse microbial communities; however, the ecological processes shaping the benthic microbial communities at the regional scale remains poorly understood. Using a high-coverage sampling strategy, 16S rRNA gene sequencing, and ecological null models, we explored variation in the ecological processes governing benthic microbial community assembly in surface sediments across an extensive Southwest Atlantic basin. The relative importance of ecological processes varied between provinces, with drift, dispersal limitation, and homogeneous selection being the three main processes that shaped the communities. Phylogenetic bin-based analysis revealed a complex balance of assembly mechanisms, with drift dominating the majority of the bin assembly of the dominant groups such as Candidatus Nitrosopumilus, Pirellula-like planctomycetes, and Woeseia. The environmental factors driving this processes were associated with sediment characteristics and organic matter quality, although they differed among provinces. Drift emerged as the dominant process, influenced by sediment grain size and depth in deeper regions and organic matter properties on the continental shelf. Dispersal limitation was linked to sediment and bottom water properties, while homogeneous selection was associated with sediment aluminum and hydrocarbon content. These findings highlight the role of spatial variation and environmental factors in benthic microbial community assembly at a regional scale, providing a framework for understanding microbial community assembly in oceanic basins, and emphasizing the need for province-specific management strategies.

Batrachochytrium dendrobatidis (Bd) is an aquatic chytrid fungus that infects amphibians and has the potential to remain viable outside of hosts. However, the role of aquatic microbiota in influencing Bd growth and survival remains insufficiently understood. In this study, we demonstrated that in the absence of amphibian hosts, aquatic environmental (AE) biofilms supported the development of Bd, allowing it to complete its life cycle for a short period; whereas aquatic planktonic microorganisms did not. However, exposure of Bd zoospores to AE biofilms or planktonic microorganisms resulted in a significant reduction in Bd DNA within a week. These results suggest a dual role of aquatic biofilms in both supporting Bd growth and inhibiting it simultaneously. Moreover, Bd monolayers, composed mainly of zoosporangia, rapidly declined when exposed to AE planktonic microorganisms. Laboratory-formulated nutrients further enhanced the Bd-inhibitory effect of AE microbiota, suggesting that competition for shared nutrients plays a role in this interaction. This study advances our understanding of the complex interactions between Bd and aquatic microbial communities, underscores the ecological significance of biofilm-associated environments, and supports the potential of microbiota-informed interventions for controlling chytridiomycosis in amphibians.

Drying is threatening global river ecosystems due to climate change, altering community composition and function even upon flow resumption. This mesocosm study investigated the greenhouse gas emissions fluxes and underlying mechanisms from benthic habitats prone to 20-100 days of drying. Results show that CO₂ and N₂O emissions from biofilms did not increase when drying increased, due to the changes in functional communities and genes. Notable is the transformation of biofilm from carbon source to sink following prolonged drying (mean emission fluxes ranged from 804.78 to -305.55 mg m² h²). This was mainly due to strong increases in the abundance of genes involved in the Calvin-Benson-Bassham cycle (2.82 × 10^-5 to 7.12 × 10^-5), and functional taxa such as gemmatimonadota and pseudomonadota. These findings reveal a potential mitigation effect of drying on greenhouse gas emissions from rivers and streams, which could be relevant in the face of climate change.

Antimicrobial resistance (AMR) is a major health concern, and a range of antibiotic and non-antibiotic agents can select for AMR across a range of concentrations. Selection for AMR is often investigated using single compounds, however, in the natural environment and the human body, pharmaceuticals will be present as mixtures, including both non-antibiotic drugs (NADs), and antibiotics. Here, we assessed the effects of one of three NADs in combination with ciprofloxacin, a commonly used antibiotic that is often found at concentrations in global freshwaters sufficiently high to select for AMR. We used a combination of growth assays and qPCR to determine selective concentrations of mixtures and used metagenome sequencing to identify changes to the resistome and community composition. The addition of the three NADs to ciprofloxacin altered the selection dynamics for intI1 compared to the ciprofloxacin alone treatments, and sequencing indicated that mixtures showed a stronger selection for some AMR genes such as qnrB. The communities exposed to the mixtures also showed changed community compositions. These results demonstrate that NADs and ciprofloxacin are more selective than ciprofloxacin alone, and these mixtures can cause distinct changes to the community composition. This indicates that future work should consider combinations of antibiotics and NADs as drivers of AMR when considering its maintenance and acquisition.

Understanding the long-term persistence of human-associated microbial signatures in burial soils offers a untapped insights into historical human health, decomposition, and ecological transformation. This study investigates whether centuries-old burial soils retain distinguishable microbial evidence of human decomposition using 16S rRNA gene sequencing on 81 samples from the New York African Burial Ground (NYABG), a 17th and 18th century cemetery for free and enslaved Africans. Comparative analyses against six control soils from nearby urban parks were conducted using QIIME2, ALDEx2, and ANCOM. Burial soils exhibited significantly greater alpha diversity (Faith's PD, Shannon, observed ASVs; P < .01) and distinct beta diversity patterns (Bray-Curtis, UniFrac; PERMANOVA P = .001). Enrichment of Firmicutes, Actinobacteriota, and gut-associated genera such as Bacillus and Ruminococcus characterized burial soils, whereas oligotrophic taxa dominated controls. Tentative identifications of human-associated pathogenic genera (e.g. Fusobacterium periodonticum, Prevotella pleuritidis) were observed exclusively in burial soils, suggesting their origin from the interred individuals but requiring further validation. These findings demonstrate that soil microbiomes reflect host-associated microbial communities long after decomposition, providing a scalable, nondestructive approach for reconstructing ancient microbial communities and host-associated health signatures. This work establishes the NYABG burial soil microbiome as a valuable model for microbial archaeology and introduces a replicable framework for integrating environmental microbiology, bioarchaeology, and historical epidemiology through the lens of postmortem microbial ecology.

Estuaries are highly productive ecosystems where microbial communities drive nutrient and carbon cycling, supporting complex food webs. With intensifying anthropogenic pressures, it is critical to understand the capacity of these communities to maintain essential functions under environmental change. Here, we examined the metabolic functions and redundancy in the microbial community of San Francisco Bay (SFB) sediments, providing the first large-scale, genome-resolved, and spatiotemporally resolved characterization of the estuary. Salinity, iron, phosphorus, sulfur, and total sediment nitrogen were significantly correlated with microbial community composition, suggesting these factors play a key role in structuring SFB communities. In support of this, we identified broad capabilities for iron cycling and key uncultured players that contribute to denitrification, nitrification, and complete nitrification (comammox). We also identified widespread capabilities for sulfur cycling, including understudied lineages capable of rDsr-mediated sulfur oxidation. SFB MAGs exhibited partitioning of multistep metabolisms, or metabolic handoffs, and the rare biosphere broadly encoded key nitrogen and sulfur cycling genes. Despite shifts in community composition across sites and fluctuations in environmental parameters, key nitrogen and sulfur metabolisms were maintained throughout the estuary, especially in nitrate reduction, nitrite reduction, and the Dsr/Sox pathway. The presence of multiple microbial taxa with similar functional roles (functional redundancy) may provide an ecosystem buffer, suggesting these functions could better recover from disturbances and ultimately contribute to the long-term health and sustainability of these vital coastal habitats.

The gut microbiota functions as a complex adaptive system where microbes form structural modules known as "guilds." Each guild comprises taxonomically distinct microbes that work together as cohesive functional units, contributing to overall system function. Traditional taxon-based microbiome analyses often yield inconsistent associations with disease, limiting mechanistic insights. To address this, we compared guild-based and taxon-based approaches using datasets from a time-restricted feeding (TRF) study in mice. C57BL/6 J male mice were assigned to ad libitum feeding or TRF groups, with metabolic parameters and gut microbiota composition assessed over 12 weeks. Isocaloric TRF improved glucose tolerance and reduced weight gain in high-fat diet (HFD)-fed mice while maintaining metabolic stability in normal-fat diet-fed mice. To examine microbial contributions, 293 prevalent amplicon sequence variants (ASVs) from the 16S rRNA gene's V3-V4 regions were clustered into 34 co-abundance groups (CAGs), representing potential microbial guilds and accounting for 96% of the total sequence abundance. By contrast, the taxon-based approach classified 660 ASVs into 126 genera, capturing only 78% of the total sequence abundance while omitting 22% of sequences representing novel microbes. The 34 CAGs preserved community-level information more effectively than the 66 prevalent genera, as demonstrated by Procrustes analysis. Five CAGs correlated with improved metabolic phenotype under TRF, including unclassifiable ASVs. Notably, two key CAGs exhibited conserved diurnal rhythmicity under TRF. In contrast, ASVs within putative health-relevant genera displayed opposing TRF responses. This study underscores microbial guilds as key mediators of TRF's metabolic benefits and emphasizes the need to recalibrate taxon-based microbiome analysis biomarker discovery.