ISME communications最新文献

Atmospheric nitrogen (N) deposition usually alters the ratio of resources to stress in terrestrial ecosystems and has important impacts on soil microbiomes. To elucidate the adaptability of soil microbiomes under N deposition scenarios, we conducted a 6-year N addition experiment in a temperate grassland in Inner Mongolia, applying different levels of ammonium nitrate (AN) and urea (AU) to form different resource-to-stress ratio. Our results reveal that the inborn high yield (Y)-resource acquisition (A)-stress tolerance (S) life history strategies of soil microbiomes collectively drive their adaptability to resources and stress under N deposition. Enriched taxa under AN treatment mainly belonged to Actinomycetota and Chloroflexota with Y and S strategies, while those under AU mainly belonged to Pseudomonadota with A and S strategies. Functional preference analysis indicated that bacterial phyla maintained consistent Y-A-S life history strategies across AN and AU treatments. Moreover, strong purifying selection restricted the pace of adaptive evolution, and horizontal gene transfer expanded the functional repertoire in a complementary rather than essential manner. Thus, the adaptation of microbiomes to shifting resources and stress under N deposition scenarios is mainly accomplished by niche conservatism ("move") rather than niche evolution ("evolve"). Our results support the point that it may be easier for microbial species to move into a befitting niche than to evolve to acclimate a new environment.

Phytoplankton are fundamental to marine ecosystems, biogeochemical cycling and climate regulation. Their community structure and productivity are shaped by biotic and abiotic factors, notably temperature and macronutrient concentrations. Climate change is altering ocean vertical stratification and nutrient dynamics, with complex and often poorly understood impacts on phytoplankton communities and global primary production. To contribute characterizing these relationships, we analysed planktonic community composition using 18S rRNA amplicon sequencing and imaging flow cytometry in the southern Indian Ocean across a strong environmental gradient from warm, stratified, N-depleted (but relatively P-repleted) waters in the north to cold, mixed, macronutrient-replete waters in the south. Phytoplankton composition and local diversity correlated primarily with temperature and macronutrient concentrations, but smaller cells (<3 μm) were less affected than larger ones (>3 μm). To disentangle the relative influence of temperature and macronutrients, we applied a model of dissolved macronutrient diffusion, suggesting that nutrient limitation, primarily nitrogen, likely constrains the growth of osmotrophic phytoplankton with cell sizes exceeding 2-15 μm in the nutrient-depleted region. We show that smaller cells, with higher surface area-to-volume ratios, are likely to evade this limitation, explaining their lower sensitivity to nitrogen concentrations, both in their taxonomic composition and diversity. Imaging flow cytometry confirmed that larger cells persisting in nitrogen-depleted waters predominantly employ alternative nitrogen acquisition strategies such as diazotrophy or mixotrophy, fostering functional local diversity. Notably, three Prymnesiophyceae taxa exhibited partial limitation by nitrogen diffusion, raising questions about their potential for mixotrophy or diazotrophy, akin to Braarudosphaera bigelowii. Other environmental factors, such as trace metal concentrations, showed weaker correlations with community structure metrics. Overall, our results are consistent with N concentration gradients and N:P imbalances driving a great share of planktonic diversity by constraining large-cell nutrient acquisition strategies and fostering functional diversification in oligotrophic regions of the Ocean.

Understanding how host and environmental factors shape gut microbiota is central to microbial ecology and evolution. However, the extent to which gut microbes covary with diet and how such variation reflects host phylogeny, remains unclear under natural conditions. Here, we used DNA metabarcoding of gut contents to analyze the dietary arthropod composition and gut microbiota of four amphibian and three reptile species from the Tarim Desert, Xinjiang, China. These species showed pronounced differences in both diet and microbial profiles. Dominant dietary arthropod families exhibited generally low overlap among species, and dietary variation did not align with host phylogeny. Interestingly, Bufotes pewzowi (amphibian) and Teratoscincus przewalskii (reptile)-the most common species in their respective groups-both primarily consumed ants (Formicidae). Conversely, gut microbial composition more closely reflected host phylogeny than diet, with a clear separation between amphibians and reptiles, particularly in the relative abundances of Bacteroidetes and the genera Bacteroides and Blautia. These findings suggest that the previously reported phylosymbiosis in these species is not primarily driven by dietary overlap. Significant diet-microbiota correlations were observed across all species and within each taxonomic class but were largely absent within species. This highlights taxonomic-level differences in the diet-microbiota relationship, indicating that diet-microbiota covariation is more pronounced over evolutionary timescales than in response to real-time dietary variation. Taken together, our results show that gut microbiota and diet exhibit distinct phylogenetic patterns, with microbiota showing both associations with diet and resilience to short-term dietary changes, underscoring the importance of considering timescales in diet-microbiota studies.

Effective wastewater treatment is of critical importance for preserving public health and protecting natural environments. Key processes in wastewater treatment, such as denitrification, are performed by a diverse community of prokaryotic and eukaryotic microbes. However, the diversity of the microbiome and the potential role of the different microbial taxa in some wastewater treatment plant setups is not fully understood. We aimed to investigate the presence and diversity of denitrifying bacteria of the candidate family Azoamicaceae that form obligate symbioses with protists in wastewater treatment plants. Our analyses showed that denitrifying endosymbionts belonging to the Ca. Azoamicus genus are present in 20%-50% of wastewater treatment plants worldwide. Time-resolved amplicon data from four Danish WWTPs showed high temporal fluctuations in the abundance and composition of the denitrifying endosymbiont community. Twelve high-quality metagenome-assembled genomes of denitrifying endosymbionts, four of which were circular, were recovered. Genome annotation showed that a newly described, globally widespread species, Ca. Azoamicus parvus, lacked a nitrous oxide reductase, suggesting that its denitrification pathway is incomplete. This observation further expands the diversity of metabolic potentials found in denitrifying endosymbionts and indicates a possible involvement of microbial eukaryote holobionts in wastewater ecosystem dynamics of nitrogen removal and greenhouse gas production.

Nitrification in aquarium biofilters transforms toxic ammonia (NH₃/NH₄⁺) into less toxic nitrate (NO₃^-) via nitrite (NO₂^-). Known freshwater aquarium nitrifiers include ammonia- and nitrite-oxidizing bacteria, ammonia-oxidizing archaea (AOA), and complete ammonia-oxidizing Nitrospira (CMX), with CMX recently shown to dominate most freshwater aquarium biofilters. However, little is known about nitrifier succession during aquarium establishment in home settings. Based on CMX prevalence in mature aquariums and the rapid growth of ammonia-oxidizing bacteria (AOB), we hypothesized that AOB initially dominate before CMX establish. To test this, we monitored microbial succession and water chemistry in three home aquariums over 12 weeks, collecting weekly samples from aquarium water, biofilter beads, and sponge filters. Biofilter DNA was analyzed via 16S rRNA gene sequencing and quantitative PCR (qPCR) targeting amoA genes. Nitrification reduced ammonia and nitrite to undetectable levels by week 3 in two aquariums and by week 8 in the third. Ammonia oxidizer detection by qPCR coincided with the onset of ammonia oxidation, with AOA preferentially colonizing biofilter beads. Metagenomic profiling of week 12 biofilter samples confirmed AOA and comammox Nitrospira amoA genes in all aquariums, along with nxrB genes from both comammox and canonical Nitrospira nitrite oxidizers. These results provide insight into the establishment of ammonia oxidizers in residential aquariums. Future work should explore factors influencing nitrifier community assembly, including inoculation sources (e.g. live plants, biological supplements), fish load, and water chemistry.

The stability of ecosystem functions under changing environmental conditions is often attributed to convergent functioning, where different mechanisms lead to similar outcomes. In soil systems, microbial activity is a major driver of nutrient cycling, yet it remains unclear whether the presence of the same genes across taxa reliably translates into redundant outcomes. We addressed this in microbial phosphate solubilization, critical when applying alternative phosphorus (P) fertilizers such as BC^plus, a biochar-based fertilizer from pyrolyzed animal bones coated with sulfur. Using multi-omics analyses, we compared two soil isolates-Bacillus licheniformis COM1 and Psychrobacillus psychrodurans INOP01-alongside the reference strain Bacillus velezensis DSM 23117. P. psychrodurans was excluded due to poor growth under P limitation. Despite similar growth and P mobilization, B. licheniformis and B. velezensis relied on distinct strategies, indicating that mechanistically diverse regulatory programs can yield convergent phosphate-solubilizing outcomes. Transcriptional changes extended beyond P metabolism, with both strains inducing nitrate reduction and adjusting sulfur metabolism, underscoring tight coupling of P, nitrogen, and sulfur cycling. B. velezensis responded rapidly by inducing Pho genes, organic acid production, nitrate respiration, and plant growth-promoting traits including indole-3-acetic acid biosynthesis. B. licheniformis instead showed a slower adaptation marked by malate-driven acidification, dissimilatory nitrate reduction to ammonium, and late riboflavin activation. While both strains solubilized phosphate, their mechanisms differed, illustrating that convergence at the functional outcome does not imply similarity in regulation or metabolism. These results highlight the need to account for strain-specific pathways when developing microbial inoculants to optimize nutrient turnover in low-input systems.

Nitrogen fixation is crucial for sustaining productivity in most of the open ocean. Cyanobacteria are the most prominent N₂-fixers, but based on the nifH gene, a marker gene of the enzyme that fixes N₂ into ammonia, non-cyanobacterial N₂-fixers often predominate the N₂-fixing community. Yet, the vast majority of them remain poorly characterized. In the oligotrophic South Pacific gyre, we found that most nifH gene sequences belonged to non-cyanobacterial N₂-fixers that dominated the waters with measurable N₂ fixation rates. Approximately two thirds of the non-cyanobacterial sequences affiliated with the group "Marine 1" which also contains the recently identified diatom symbiont Ca. Tectiglobus diatomicola, a heterotrophic bacterium belonging to the order Rhizobiales, and its closest relative, Ca. Tectiglobus profundi. Using fluorescence in situ hybridization and electron microscopy, we found that Ca. Tectiglobus-diatom symbioses were present throughout the gyre. These diatom symbioses were also present in samples devoid of nifH from Ca. T. diatomicola and Ca. T. profundi indicating that other members of the "Marine 1" group are also diatom symbionts. At least two morphologically distinct diatoms harbored Ca. Tectiglobus symbionts, revealing a so far unknown diversity in hosts for these rhizobial N₂-fixers. Single-cell activity measurements showed that Ca. Tectiglobus-diatom symbioses actively fixed nitrogen and could account for up to 40% of the N₂ fixation in the South Pacific gyre. Given the size of the largest oceanic biome and the abundance of Ca. Tectiglobus-related nifH genes in other ocean regions, these heterotrophic N₂-fixers likely play a major role in marine nitrogen cycling.

Deep oligotrophic lakes hold over 80% of global lake water. In their hypolimnion, ammonia oxidation (the first step of nitrification) and non-photosynthetic fixation of dissolved inorganic carbon (DIC) are key processes, presumably linked by large populations of ammonia-oxidizing archaea (AOA). We used stable isotope-based activity measurements to follow both processes below the thermocline and in the central hypolimnion in deep oligotrophic Lake Constance. Throughout seasons, they varied substantially below the thermocline peaking at 139.0 NH₄ ⁺ nmol l^-1 d^-1 oxidized and 14.6 nmol DIC l^-1 d^-1 fixed. At the center of the hypolimnion, they were rather stable averaging 7.5 nmol NH₄ ⁺ l^-1 d^-1 and 1.3 nmol DIC l^-1 d^-1, respectively. However, both processes did not correlate in their spatiotemporal and temperature-related dynamics. Temperature manipulations (5-20°C) confirmed this disconnect with ammonia oxidation peaking at 10°C while dark DIC fixation increased exponentially with temperature. DIC fixation of single AOA cells centered at 2.17 × 10^-18 mol C cell^-1 d^-1, explaining only 11% of overall DIC fixation. Metatranscriptomic analyses supported this, revealing that most DIC-fixation pathway transcripts originated from RubisCO-encoding cryptophytes, cyanobacteria, and Alpha- and Betaproteobacteria, rather than AOA or other nitrifiers. These non-nitrifier groups likely activated the Calvin cycle to maintain redox balance in the dark. Our findings provide a new perspective on nitrification-driven chemolithoautotrophy in oligotrophic lake hypolimnia, with freshwater AOA contributing a minor part to dark DIC fixation, likely explaining decoupled dynamics of ammonia oxidation and dark DIC fixation.

Ixodes frontalis, an ornithophilic tick species, is widely distributed all over Europe exhibiting two genetically diverging haplogroups based on differences in the cytochrome c oxidase subunit 1 mitochondrial gene. Despite its broad distribution, little is known about the presence of symbiotic bacteria in I. frontalis, while symbionts are generally widespread in ixodid ticks and responsible for important effects on host fitness. We collected I. frontalis from France and Italy (n = 277) and assessed that the most prevalent haplogroup was A (73%). We then investigated the presence of the symbionts, Midichloria mitochondrii and Spiroplasma ixodetis. They were both found at a high prevalence in adult ticks (66% and 77% respectively), while the number of positive immature ticks was significantly lower (18% for both). The experimental analysis of larvae hatched from egg clutches obtained from four females hints at vertical transmission of both symbionts. We obtained three genomes of Spiroplasma and one of Midichloria, and used them to perform comparative genomic analysis. Average nucleotide identity among available Spiroplasma or Midichloria genomes from I. frontalis are all extremely high, suggesting low genetic variability for both symbionts. Gene presence/absence analysis confirmed the presence of B vitamin synthesis genes in the genome of M. mitochondrii, and also showed the presence of the ETX/MTX2 gene, the RIP family and a partial Spaid-like gene in S. ixodetis. This gene repertoire indicates a nutritional role for Midichloria, while for S. ixodetis we hypothesize a role of this bacterium as a defensive symbiont or a manipulator of the host reproduction.

Seaweed microbiomes are diverse and frequently species-specific. By actively attracting and repelling settling bacteria through exuded metabolites, seaweeds are thought to exert a strong selective pressure on their microbiomes. However, to what degree seaweed-associated bacteria are adapted to their host has received little attention. Here, we retrieve cultivable seaweed bacterial communities from Palmaria palmata (Dulse) and Fucus serratus (Serrated Wrack) and use reciprocal transplant experiments to test whether bacterial isolates have the greatest fitness on their host seaweed species. We used agar derived from host seaweed extracts for bacterial isolation, which was found to be superior to a generic marine agar formulation based on both 16S rRNA gene amplicon alpha- and beta-diversity comparisons to uncultured samples. We then demonstrate that bacterial isolates from both seaweed species exhibit higher fitness in media derived from their native host compared to a non-native host. Although epibacterial fitness varied between hosts, bacterial isolates on average outperformed non-native counterparts in their native environment. By integrating amplicon sequencing with laboratory experiments, we demonstrate that bacteria are locally adapted to their seaweed host species. These findings contribute to the growing body of research exploring the evolutionary and ecological drivers that shape bacterial communities, with implications for ecosystem management, disease control, and microbial biotechnology.