Microbial Ecology最新文献

High-latitude ecosystems are undergoing rapid ecological changes in response to climate warming. While some changes are well studied, the responses of microbial communities remain less understood. Testate amoebae, shell-producing protists well preserved in peat, provide a means to reconstruct past microbial dynamics. Mixotrophic taxa such as Archerella flavum host algal endosymbionts (zoochlorellae), allowing both heterotrophic and phototrophic energy acquisition. Previous work has demonstrated that these pathways result in different δ¹³C values. We applied a novel stable isotope approach to a peat core from the North Slope of Alaska to reconstruct changes in phototrophy by Archerella flavum. δ¹³C values were measured on Archerella flavum tests (i.e. shells) and Sphagnum, and a two-endmember mixing model was used to estimate relative usage of phototrophy through time. δ¹³C values were compared with testate amoeba community composition, test size, vegetation, and historical climate. Archerella flavum δ¹³C values were consistently more positive than Sphagnum δ¹³C values in the peat core, and patterns indicated greater phototrophy use after the late 1980s CE. This shift was followed by expansion of Archerella flavum populations and a trend of decreasing test length in several testate amoeba taxa. Increased phototrophy was associated with higher peat C:N ratios, indicating more oligotrophic conditions. From 2007 to 2019 CE, the length of the snow-free growing season was correlated with estimates of phototrophy usage, with more phototrophy during longer growing seasons. δ¹³C analyses of mixotrophic testate amoebae are a powerful tool for reconstructing microbial nutritional strategies and responses to past environmental change.

Understanding local adaptation of phytopathogens has significant practical and economic implications. The opportunistic pathogen Pseudomonas syringae exemplifies this challenge, causing regular epidemics in diverse host plants. Many pathogenic microbes, including P. syringae, are divided into intraspecific lineages, or pathovars, based on their host-of-isolation. However, whether pathovar classifications reflect adaptation of the pathogen to the host (local adaptation) or a competitive advantage of the pathogen in the host (local dominance), often goes untested. In this study, we performed in vitro growth assays and factorial controlled infections to test whether a suite of five P. syringae pathovars are locally adapted to, and/or locally dominant in, their hosts-of-isolation. We found evidence of local adaptation in three of five pathogens, only one of which was also locally dominant. Several strains performed as well or better than the locally adapted strain in that strain's host-of-isolation, consistent with cost-free generalism. Thus, pathovar designations do not reliably delineate pathogenic phenotypes. Moreover, we found that in vitro growth was not predictive of in planta growth. To contextualize phenotypes, we compared pathogen gene content, identifying unique phytotoxins, secreted effectors, and general virulence factors. In all, we found that local adaptation is common but not universal, and that locally adapted strains are not necessarily constrained from performing competitively in multiple hosts. Thus, neither host-of-isolation nor in vitro performance is reliable for strain classification. Our findings highlight the vast intraspecific variation in P. syringae, and the coexistence of multiple successful adaptive strategies.

Antimicrobial resistance (AMR) is a growing global challenge that compromises the effectiveness of disease control and increases risks for both human and animal health. Aquaculture systems are particularly vulnerable, as extensive and often inappropriate antimicrobial use has driven the emergence and persistence of multidrug-resistant bacteria. This mini-review summarizes the ecological and genetic mechanisms underlying AMR in aquaculture, with emphasis on plasmid-mediated resistance and its role in horizontal gene transfer. It also addresses the broader environmental and public health implications of these processes and calls for sustainable management, enhanced surveillance, and coordinated international policies to curb resistance dissemination and safeguard global food security.

Nitrogen availability limits primary production in the Arctic Ocean, making it vital to understand its sources and sinks to predict future productivity. Although nitrogen fixation has been reported in the Arctic Ocean, data remain scarce, especially in the Atlantic sector. Here, we measured nitrogen fixation rates and examined diazotroph community composition across the Fram Strait, targeting Polar waters in the East Greenland Current, Atlantic waters in the West Spitsbergen Current, and their frontal zone. Nitrogen fixation was mainly low (< 1 nmol N L^-1 d^-1) in Polar waters, however, elevated at the one station in the Atlantic water sector (up to 10.15 nmol N L^-1 d^-1). Rates were only detectable in the epipelagic layer (0-100 m) across the strait and positively correlated with temperature, primary production, and chlorophyll-a fluorescence, and negatively correlated with coloured dissolved organic matter and silicate. The diazotrophs were dominated by non-cyanobacterial diazotrophs (NCDs; 77% of nifH amplicon reads), with an Arctic Betaproteobacterial group (order Rhodocyclales) accounting for 11% of sequence reads. This group was quantifiable (up to 6700 nifH gene copies L^-1) within the West Spitsbergen Current and the frontal zone, where the highest nitrogen fixation and primary production occurred, and its prevalence was positively correlated with temperature. We propose that temperature and freshly produced dissolved organic matter influence the NCD-dominated nitrogen fixation in Fram Strait. Our study suggests that NCDs are key diazotrophs in Fram Strait, and that nitrogen fixation rates and their potential importance for primary production vary across the contrasting water masses entering and exiting the Arctic Ocean. We encourage future studies to quantify these nitrogen fluxes and evaluate their importance for productivity in the Arctic Ocean.

The olive tree (Olea europaea L.) hosts diverse endophytic microbial communities that contribute to its resilience, productivity, and adaptation to environmental stressors. Since the temperature increases caused by global climate change primarily affects the aerial part of the plant, this review synthesizes current knowledge on the diversity, composition, and ecological drivers of olive phyllosphere endophytes, with a focus on bacterial and fungal communities. We highlight the role of host-related factors-including plant genotype, organ specificity, age, and phenological stage-in shaping microbiota structure across spatial and temporal scales. Genotype consistently emerges as a major determinant of microbial composition, while leaves and twigs harbor distinct yet overlapping communities. Geographic location, environmental variables, and seasonal shifts significantly influence microbial assemblages, with closer sites often supporting more similar communities. We also discuss the impact of agricultural practices and biotic and abiotic stressors on microbiota stability and function. Notably, several cultivable taxa-including Bacillus, Paenibacillus, Pantoea, Aureobasidium, and Penicillium-exhibit antagonistic activity against key olive pathogens, underscoring their potential as biological control agents. We conclude by emphasizing the need for functional studies to elucidate the roles of keystone endophytes and to inform microbiome-based strategies for sustainable olive cultivation.

Although phages shape bacterial evolution and physiology, the specificity of host transcriptomic responses to phage infection remains incompletely understood. Here, we performed global transcriptomic profiling of Escherichia coli exposed to two lytic phages, ΦX174 and T4, and the temperate phage λ, to explore both conserved and phage-specific host responses. All infections induced stress-related genes, including SOS and general stress pathways, along with repression of anabolic processes such as purine and amino acid biosynthesis, suggesting a metabolic shift to conserve resources. Notably, ΦX174 strongly activated the phage shock protein operon, while both ΦX174 and λ selectively induced soxS, a regulator of oxidative stress. Despite infecting the same host, each phage triggered distinct transcriptional signatures. These findings highlight the complexity of bacterial responses and the value of transcriptomics in decoding host-phage interactions, offering insights into resistance, survival, and co-evolution.

Warming is altering the functioning of desert ecosystems in global drylands. Microbial communities are crucial for maintaining these ecosystems, yet how their co-occurrence networks and assembly mechanisms respond to warming remains unclear. Using 16 S and ITS rRNA amplicon sequencing, we examined bacterial and fungal community composition and structure. Further, we investigated cross-trophic bacterial-fungal interactions via inter-domain ecological network analysis. Warming significantly altered the diversity, composition, and structure of both bacterial and fungal communities. It increased bacterial network complexity but simplified the fungal network. Notably, warming enhanced cross-trophic interactions between bacteria and fungi, facilitating the maintenance of microbial hierarchical interactions, particularly bacterial network complexity. However, microbial keystone taxa declined dramatically under warming, 41.18% of these belonged to Ascomycota. Neutral community models and normalized stochastic ratio-based analyses revealed that deterministic processes dominated community assembly, with warming increasing their relative importance by 8-46%. This suggests a potential deterministic environmental filtering induced by warming. Collectively, these findings advance our understanding of the ecological mechanisms and microbial interactions underpinning rhizospheric communities in drylands under future climate change.