ISME communications最新文献

Diatoms, a diverse and abundant group of microalgae, play a crucial role in the functioning of rivers, and are widely used as indicators of ecological quality. This microalgae group has an intraspecific genetic diversity that is poorly understood on a global scale. We examined their genetic diversity using metabarcoding data from Nordic to Equatorial rivers (n = 1103 samples). Notably, 61% of genetic variants were endemic to a single climate zone, including 33% from the Equatorial zone. Looking at the genetic diversity within species, one third of the species showed geographic pattern between climate zones and the phylogenetic structure of their communities indicated that they were shaped by environmental filtering. Another third showed no geographic pattern, and their communities were in majority shaped by neutral processes. A final group was between these two situations. Interestingly, no geographic pattern was observed within the same climate zones, even in regions over 10 000 km apart. We conclude that the numerous species showing allopatric diversification between climate zones, would deserve to be separated into new species to improve diatom-based biomonitoring tools. For future studies, expanding geographical sampling coverage, together with using multi-markers or metagenomes approaches would enable to go beyond these results.

Interkingdom interactions are crucial for community and ecosystem function; however, the secondary metabolites mediating interactions between plant beneficial bacteria and fungi remain understudied. Beneficial Penicillium and Bacillus species can individually suppress soilborne phytopathogens and promote plant growth. Here, we showed that Penicillium hordei and Bacillus subtilis co-culture led to precipitation of B. subtilis lipopeptides, observed as white lines in agar. Metabolomic analysis revealed that the presence of B. subtilis enhanced the production of fungal terrestric acid and its biosynthetic intermediates, which in turn induced lipopeptide precipitation, preventing P. hordei inhibition through chemical inactivation and physical barrier formation. Besides lipopeptide precipitation, terrestric acid-mediated acidification progressively reduced production of antifungal plipastatins. The lack of lipopeptide production permitted P. hordei to invade and overgrow the B. subtilis colony. We demonstrated that the white line phenomenon was conserved among closely related fungi via secretion of terrestric, fulvic, or barceloneic acids. Furthermore, terrestric acid at specific concentrations acted as a universal metabolite that drives B. subtilis lipopeptide precipitation even in distantly related fungi. This study provides new insights into acidification as a fungal defensive strategy that may promote co-existence with beneficial bacteria exhibiting strong antagonistic potential, thereby contributing to the formation of a stable rhizosphere community.

Blastocystis is a prevalent gut eukaryote intricately associated with the gut microbiota. This genetically diverse protozoan exhibits significant intra-host subtype heterogeneity, yet the implications of this diversity for the host gut microbiome remain poorly understood. Here, we investigated the interactions between Blastocystis and gut microbiota in non-human primates at the level of subtypes, using a comprehensive investigation of gut microbiota for Blastocystis carriers of captive Macaca fascicularis (discovery cohort, n = 100) and Macaca mulatta (validation cohort, n = 26). We identified highly prevalent intra-host co-occurrence patterns of Blastocystis SSU rRNA-based subtypes, primarily dominated by Subtype 1 (ST1) or ST3. These patterns were associated with compositional and structural variations in the gut microbiome but were not significantly influenced by host covariates such as sex, age, or BMI. Specifically, Ruminococcaceae-enterotype was enriched in the patterns dominated by ST1, whereas Limosilactobacillus-enterotype was predominantly identified in the patterns dominated by ST3. Variance partitioning and mediation analyses revealed that the absolute abundance of Blastocystis was a critical determinant in elucidating this microbiota association across subtype concurrent patterns. In vivo experiments in a new cohort (n = 11) demonstrated that lactic acid bacteria, enriched in the Limosilactobacillus-enterotype, were sufficient to reduce Blastocystis load. We validated the strong association between gut microbiome composition and Blastocystis load in M. mulatta, confirming that specific microbial features could quantitatively predict Blastocystis status in both species. These findings highlight the close links of the gut microbiome with within-host subtype diversity patterns and absolute abundance of Blastocystis.

Unveiling the soil biological communities ecologically associated with crop wild progenitors (CWPs) in their habitats of origin is essential for advancing productive and sustainable agriculture. A field survey was conducted to investigate the edaphoclimatic conditions and soil bacterial, fungal, protist, and invertebrate communities of 125 populations of direct progenitors of major crops for world agriculture. The wild populations clustered into four ecoregions shaped by two edaphoclimatic dimensions: one summarizing variations in soil sand contents and nutrients concentrations, and the other featuring changes in aridity, soil pH, and carbon storage potential. We identified a common soil core community across CWPs that varied significantly along deserts to tropical seasonal forests and savannas. The assembly of the soil core community was driven by varying environmental preferences amongst soil biodiversity kingdoms, reflecting potential shifts in their functional profiles. The tropical ecoregion exhibited higher proportion of acidophilic bacteria, fungal, and protist parasites, whilst desert ecosystems harboured greater abundances of saprophytic fungi and heterotrophic protists. Moreover, CWPs displayed unique microhabitats that incorporate variability into the soil community assembly. Our work reveals the biogeography of soil communities associated with CWPs, the first step towards the development of microbial rewilding initiatives.

Elemental sulfur disproportionation is an ancient microbial metabolic process, and the phylogenetic distribution of elemental sulfur disproportionators may be broader than previously thought. We enriched a bacterial community capable of this process, with Exiguobacterium making up 99.45% of the total population. The results indicate that Exiguobacterium facilitates the formation of thiosulfate and sulfide through elemental sulfur disproportionation. This study represents the first report documenting elemental sulfur disproportionation by Bacilli. Metagenomic analysis shows that rhodanese-like sulfur transferase genes are significantly more abundant in the experimental group than in the control group, suggesting that they are implicated in elemental sulfur disproportionation in Exiguobacterium. These findings support the idea that Bacilli and/or Firmicutes are the oldest extant bacterial phyla. Our research fills a critical gap in understanding sulfur biogeochemical cycles. Given the widespread occurrence of Exiguobacterium across various environments, direct microbial transformations between elemental sulfur and thiosulfate are likely prevalent throughout ecological systems.

Nitrification is the two-step microbial oxidation of ammonia to nitrate via nitrite, and it can contribute to environmental problems in soils. Some nitrifiers have been cultivated from acidic soils at pH <5.5, allowing their metabolic potential and phylogeny to be investigated through genomic analyses. However, the genomic features of the genus Nitrospira remain poorly understood in the context of acid tolerance, despite its wide distribution in acidic environments. This study aimed to characterize the physiology and genomics of acid-tolerant Nitrospira enriched from an acidic soil. Using a metagenomic approach, two closed genomes of Nitrospira were reconstructed: a complete ammonia-oxidizing (comammox) bacterium and a nitrite-oxidizing bacterium (NOB). Both enriched Nitrospira survived at pH <5.5 in physiological tests, and the enriched comammox Nitrospira was phylogenetically close to clones derived from acidic soils. The active-site residues of hydroxylamine oxidase, a key nitrification enzyme, were conserved between the comammox Nitrospira characterized in this study and the previously reported betaproteobacterial ammonia oxidizers. This conservation suggests that existing nitrification inhibitors targeting this enzyme may also inhibit ammonia oxidation by comammox Nitrospira in acidic soils. Although the comammox and NOB Nitrospira in this study shared nearly all key metabolic pathways with Nitrospira species identified from neutral pH environments, both possessed passive urea transporters homologous to those found in acid-tolerant bacteria. These results revealed the acid tolerance of the enriched Nitrospira at pH <5.5, as well as their genomic features shared with acid-tolerant bacteria, rather than with previously reported Nitrospira species.

The remineralization of organic matter by benthic bacteria is an essential process in the marine carbon cycle. In polar regions, strong variation in daylength causes pronounced seasonality in primary productivity, but the responses of sedimentary bacteria to these fluctuations are not well understood. We investigated the seasonal dynamics of benthic bacterial communities from an Arctic fjord and found a partitioning of the communities into seasonally responsive and stable guilds. We separately analyzed the fractions of cells in the porewater and those loosely and firmly attached to sand grains through 16S ribosomal RNA gene sequencing, cell counting, rate measurements, and geochemical analyses. The porewater and loosely attached bacterial communities showed a dynamic response in composition and activity, suggesting that they play a central role in benthic-pelagic coupling by responding rapidly to seasonal fluctuations in organic matter availability. In contrast, the majority of the firmly attached cells showed a more buffered response, as reflected, e.g. in the consistently high cell numbers of Woeseiaceae. This fraction is potentially key to maintaining baseline remineralization processes throughout the year, independent of fresh organic matter input. These findings provide a new mechanistic understanding of carbon cycling in Arctic surface sediments that may also apply beyond polar regions.

Robust interspecies interactions are essential for efficient methanogenesis in anaerobic digestion. This study investigated the impact of quorum sensing (QS) enhancement on the succession of methanogenic communities during anaerobic digestion. The QS stimulation via exogenous N-acyl-homoserine lactones enhanced methane production by 18.8%-22.1%. Moreover, QS shaped microbial community succession toward a more deterministic assembly, selectively enriching key syntrophs (Pelotomaculum, Smithella), and methanogens (Methanobacterium, Methanothrix). Metagenomic analysis revealed that QS induced genes related to transcription, transport, and cofactor biosynthesis instead of directly regulating carbon metabolism. In this context, interspecies electron transfer emerges as a critical factor regulating interspecies interactions under QS regulation. Specifically, QS enhancement boosted redox mediator secretion, and the concentration of 2-amino-3-carboxy-1,4-naphthoquinone and phenazine increased by 7.8- and 4.8-fold, respectively. QS enhancement also induced higher abundance of c-type cytochromes. Moreover, the higher electron transfer coefficients were detected with 40.2%-89.9% increase. Further, QS also enhanced relative abundance of genes involved in Complex I/III and ferredoxin-dependent hydrogenases, promoting electron flow from syntrophs to methanogens. These effects induced higher relative abundance of genes associated with syntrophic propionate/butyrate oxidation and hydrogenotrophic/acetotrophic methanogenesis. Collectively, given that the similar regulation pathway is widely distributed in anaerobes, these findings identify QS as a critical ecological signal that drives functional microbial succession.

Successional pathways of microbial communities are influenced by the complex interactive dynamics among the resident and immigrating species, along with the interactive feedback loops with their environment. Although studies on microbial communities have described patterns of microbial succession, quantitative evidence of how resident communities respond to immigrating species and how such relationships translate into successional changes remains limited, especially for species-rich communities under natural settings. Here, we carried out a field experiment to investigate how the identity of immigrating species influences the successional pathways of wood-inhabiting fungi. We simulated immigration through inoculations of nine selected wood-inhabiting fungal species and characterized resident fungal communities before and one and two years after the inoculations through DNA metabarcoding. The experiments included 275 naturally fallen and 185 artificially felled fresh logs of Norway spruce, with different log types hosting distinct initial resident communities of fungi and representing different abiotic conditions. While the resident community succession was mostly explained by the log-level abiotic characteristics, the identity of immigrating species also influenced the composition of resident communities, and consequently community succession. The immigrating species influenced resident species mostly negatively, suggesting competitive interactions to be important determinants of community succession. The responses of resident species to the immigrating species were phylogenetically correlated, suggesting that shared traits underlie species interactions in the species-rich wood-inhabiting fungal communities. This study advanced the understanding of community succession in species-rich natural systems by providing experimental evidence that the immigrating species influence community succession through the phylogenetically structured responses of resident species.

Nutrient niche access by the gut microbiota impacts community assembly and dynamics, the production of host-benefiting short-chain fatty acids (SCFAs), and pathogen inhibition through colonization resistance. Furthermore, deciphering if and how niche access varies on a strain level will be important as individual strains of gut microbes are selected for inclusion in new live biotherapeutic products. Despite this, for many gut anaerobes, nutrient niche occupancy and impacts of strain variation remain unknown. Here, we examined nutrient niches of Anaerostipes hadrus (AH), a butyrate-producing member of the Lachnospiraceae family. We found that AH isolates encode a carbohydrate metabolism gene repertoire that is distinct from other Lachnospiraceae. Furthermore, tested AH isolates show variation in carbohydrate-related genes between strains and large numbers of genes associated with horizontal gene transfer events. Functionally, we demonstrate that AH isolates exhibit strain-specific patterns of nutrient niche access that can be associated with the gain, loss, and disruption of gene clusters enabling specific carbohydrate metabolism. This strain-specific carbohydrate use drives variable SCFA production. Unexpectedly, strains exhibit differential preferences for carbohydrates, which alter SCFA profiles in environments with multiple possible nutrient niches available. Furthermore, when strains of AH interact in an environment with multiple nutrient niches available, strain-strain interactions result in varying SCFA profiles that extend beyond the additive effects of individual strain behavior. Altogether, these results demonstrate the importance of evaluating strain-level variation in the design of future live biotherapeutic products.