Environmental Microbiology Reports最新文献

Cornflower (Centaurea cyanus L.) is a widespread weed in cereal crops and is commonly controlled with sulfonylurea herbicides. In Poland, populations of cornflower resistant to acetolactate synthase inhibiting herbicides, such as tribenuron-methyl, have been increasingly reported. Both target-site and non-target-site resistance mechanisms may contribute to this phenomenon. Plant-associated microorganisms are known to play essential roles in alleviating abiotic stress. Moreover, weeds are considered reservoirs of plant pathogenic viruses. Since bacteria and viruses associated with cornflower have not been analysed to date, data mining was undertaken to identify viral and bacterial sequences in metatranscriptome datasets obtained from plant biotypes that are both susceptible and highly resistant to tribenuron-methyl. Using MEGAN6 and Kraken2, taxonomic classification revealed the presence of sequences of two double-stranded RNA viruses belonging to the family Partitiviridae, which have not been described before. For bacterial sequences, 19 genera were identified, including Bacillus, Mesorhizobium and Acinetobacter, some of which are associated with plant growth promotion or xenobiotic degradation. Although the presence of partitiviruses was unrelated to herbicide resistance status, some bacterial genera (e.g., Rothia) were more abundant in resistant than in susceptible plants. These results suggest that those bacterial genera present in weeds may be involved in counteracting ALS-inhibiting herbicides.

Axenisation of phototrophic eukaryotic microalgae has been studied for over a century, with antibiotics commonly employed to achieve axenic cultures. However, this approach often yields inconsistent outcomes and contributes to the emergence of antibiotic-resistant microbes. A comprehensive analysis of previous reports on axenisation was necessary to identify alternate workflows tailored to each major microalgal group. Literature from scholarly databases was systematically recovered and network component analysis was performed to identify method-clusters commonly reported for the axenisation of diatoms, dinoflagellates, and green algae. Promising workflows circumventing the use of antibiotics appeared to be filtration ↔ washing ↔ micropicking for diatoms, and micropicking ↔ subculturing ↔ flow cytometry for dinoflagellates. No clear workflow could emerge for green algae although Streak plating ↔ Flowcytometry → Ultrasonication was considered despite these methods appearing in different clusters. Furthermore, the literature suggests that a combination of microscopy (e.g., epifluorescence), cell counting (e.g., agar plating), and sequencing (16S and/or 18S) was essential to confirm the final purity of the mother culture. More systematic and high-quality primary research is required to identify effective workflows for other microalgal divisions and fortify/contrast the ones proposed herein based on network component analysis.

To be considered ultimately biodegradable, a substance needs to reach ≥ 60% mineralisation in screening tests. Ultimate biodegradability can also be studied with targeted studies, for example, using an inoculum after enrichment or isolated bacteria. Here, degradation of 2-cyclohexylidene-2-phenylacetonitrile (Peonile) was studied. Peonile is composed of biodegradable substructures and does not have typical nonbiodegradable motifs, such as extensive alkyl-branching or quaternary carbon atoms, yet it fails ready biodegradability tests. An adapted sludge was able to mineralise Peonile with a bi-phasic curve. Two Acidovorax strains isolated from this inoculum degrade the phenyl ring of Peonile, generating the metabolite 2-cyano-2-cyclohexylideneacetic acid. A Variovorax strain degrading this metabolite was isolated at the end of a mineralisation experiment with the adapted inoculum. A mixture of both bacteria was shown to mineralise Peonile under OECD 301D and 301F incubation conditions. The need for cooperative action of two bacteria explains the bi-phasic curve in the mineralisation by the adapted sludge and indicates that Peonile is ultimately biodegradable by bacteria originally present in sewage sludge. This is one of the first examples showing cooperative mineralisation of a xenobiotic by specific bacteria in sewage sludge.

Investigating the work-environmental microbiome is critical for assessing occupational risk associated with exposure to microorganisms. The present study examined the bacterial composition of inhalable dust from waste sorting plants and explored their potential to induce Toll-like receptors (TLR) in vitro, thereby providing insights into the immunomodulatory potential of complex microbial communities from occupational settings. These findings highlight how few dominant bacterial species shape the immune activation properties of the overall bacterial community, where less abundant taxa play a crucial role in immune modulation through TLR activation. The strong association between TLR activation and rare yet highly inductive bacterial taxa demonstrates their potential immunological significance, suggesting that even low-abundant microbes may have a disproportionate impact on immune responses and occupational health outcomes.

Size fractionation, filtering water sequentially through a large (3 μm) and fine (0.2 μm) pore size filter, is a widely applied approach to target specific microbial size ranges, differentiating between particle-associated, and free-living microorganisms. To characterise its impact on microbial diversity and its comparability to unfractionated samples, we analysed 16 weekly ocean samples across five depths during a phytoplankton spring bloom. We used a universal marker to characterise prokaryotes, eukaryotes and chloroplasts in unfractionated (> 0.2 μm), fractionated (large > 3 μm, small 0.2-3 μm) and de-fractionated samples, the reconstitution of the small and large fractions. The particle-associated fraction was the most different community from all other samples, and de-fractionating before or after sequencing results in a community that is most similar to unfractionated samples in terms of composition and richness with the exception of very rare taxa. Across all depths and weeks, 75%-97% of ASVs were shared, but some discrepancies in relative abundances were unresolved, including for some lineages of free-living Bacteroidota. Community composition differences from size fractionation were more pronounced during the bloom period in comparison to pre-bloom. Differential-abundance analysis detected at most one significantly different ASV between fractionated and de-fractionated samples, highlighting the similarity in community composition and temporal dynamics between the fractionated and de-fractionated sets.

Spongospora subterranea f. sp. Subterranea (Sss), the causal agent of powdery scab in potatoes, is a globally important soil-borne pathogen with an obligate biotrophic lifestyle and long-lived resting spores that make it difficult to control. This paper compiles and evaluates all currently available molecular resources for Sss, including genomic, transcriptomic, proteomic, and metabolomic datasets, providing the first comprehensive overview of the pathogen's molecular research landscape. Although recent long-read assemblies have advanced the Sss genome, it has not yet reached chromosome-level resolution. A large proportion of predicted proteins remain uncharacterised, restricting the ability to identify effective targets for breeding or chemical control. Compared to other major plant pathogens, Sss remains severely under-resourced at the molecular level. This paper also summarises studies that have applied molecular tools to investigate resistance in the potato host, revealing early insights but underscoring the need for more extensive research. Overall, this short review identifies key gaps in molecular knowledge and highlights the need for a high-quality, chromosome-level reference genome and improved annotation through post-genomic analyses to support more effective and targeted management strategies for powdery scab disease of potato.

Associations with fish can benefit corals by increasing growth and stress tolerance. To investigate microbial and nutritional responses of corals to fish associations in the context of enhancing coral aquaculture outcomes, Pocillopora verrucosa were cultured for 3 months with different combinations of live feeds and schools of juvenile Chromis viridis damselfish. The combined live feeds and fish treatment resulted in a bacterial community most similar to wild P. verrucosa, dominated by Endozoicomonas-affiliated taxa. Protein content was enhanced in corals with access to live feeds and/or dissolved fish wastes compared to unfed controls. Total lipid concentrations were elevated in captive corals with access to dissolved fish wastes and at moderate levels in those supplied live feeds, likely due to the activity of corals' symbionts and deposition of derived lipids from live feeds, respectively. However, all captive corals demonstrated a significant reduction in storage lipid concentration compared to samples from the wild. Fatty acid analysis indicated these shifts were likely the result of higher light levels in the field supporting Symbiodiniaceae photosynthesis and potentially feeding on wild zooplankton. Co-culturing captive corals with fish and providing appropriate live feeds may therefore offer an effective approach to improve coral nutrition, health and microbiome stability.

Yeasts are remarkably versatile microorganisms whose applications reach far beyond their traditional roles in fermentation. In recent years, they have also emerged as valuable tools in areas related to biosecurity and civilian protection. This paper explores how both conventional and non-conventional yeast can contribute to the detection, neutralisation, and prevention of biological and chemical threats. We review the use of recombinant yeast cells in biosensors for heavy metals, organic pollutants and endocrine-disrupting compounds, as well as their role in bioremediation and toxin removal. Special attention is given to the development of yeast-based vaccine platforms, including RNA and antigen-display systems using Saccharomyces cerevisiae and Komagataella phaffii. These technologies illustrate how yeast can bridge biotechnology and security, offering low-cost, scalable and sustainable solutions. However, practical deployment still faces challenges such as biosensor stability, regulatory barriers for genetically modified strains and the need for standardised calibration. Altogether, yeast biotechnology is positioned as a promising and resilient component of future biodefense and environmental protection strategies, strengthening preparedness in the face of hybrid biological and chemical threats.

The forces shaping host specificity in the animal gastrointestinal microbiome (AGM) are often studied through separate lenses: community-level patterns (phylosymbiosis) or lineage-level histories (cophylogeny). Furthermore, traditional diversity metrics fail to capture compositional heterogeneity from host-specific distributions. We bridge these gaps using our SSD (Species Specificity and Specificity Diversity) framework, a recent conceptual and computational advance that quantifies host specificity across scales via: (i) Species Specificity (SS), locating species on the specialist-generalist continuum; (ii) Specificity Diversity (SD), quantifying community compositional heterogeneity; and (iii) statistical tests for identifying unique/enriched species. Applying SSD to 4903 AGM samples from 318 species, we identified unique and enriched microbial species in specific host taxa and diets, demonstrating that host phylogeny and diet jointly shape these patterns. A PTSD (Phylogenetic Timeline–Specificity Diversity) power-law model reveals the evolution of more complex microbiome structures in modern species. One surprising finding is the high similarity amongst animal AGMs, with only 252 microbial species being exclusively unique at the animal class level—somewhat analogous to the high genomic similarity between humans and primates. Our findings demonstrate a unified quantitative approach to dissecting the eco-evolutionary forces that shape microbial specificity and specificity heterogeneity, with potential synthesis with established phylosymbiosis and cophylogeny frameworks.

Carboxydotrophic acetogens are found widespread in the environment, yet the strains characterised to date are almost exclusively mild acidophiles or neutrophiles, often isolated from gut or freshwater systems. Here, we describe a novel carboxydotrophic halo-alkaliphilic, acetogenic bacterium, strain MD4, isolated from a CO-fed bioreactor operated under high salt and alkaline conditions. Phylogenetic analysis suggests that strain MD4 is the first representative of a novel genus, branching between the Alkalibacter and Alkalibaculum genera, for which we propose the name Haloacetibacter carboxydivorans. The bacterium tolerates a wide range of sodium (0.01–2.5 M) and pH (7–10), but was not exceptionally tolerant to metals such as copper, nickel and cobalt. During growth on CO, strain MD4 produced formate and acetate, the former being co-consumed upon low CO availability to drive acetogenesis. Interestingly, common by-products of carboxydotrophic acetogenesis—ethanol or hydrogen—were not produced, suggesting that formate production may serve as a form of redox homeostasis during alkaliphilic carboxydotrophy. Genome analyses revealed no clear bifurcating formate dehydrogenase or formate hydrogen lyase, but during carboxydotrophy the transcriptome showed high expression of two putative bifurcating hydrogenases, and a NADH-dependent formate dehydrogenase, potentially playing a role in the dynamic formate metabolism.