Environmental microbiology最新文献

The growing research into the archaeal lipidome has uncovered a remarkable structural diversity in isoprenoidal glycerol dialkyl glycerol tetraethers (iGDGTs) and revealed complex membrane adaptations, especially in extreme environments. We performed a comprehensive analysis of the lipidome from the subsurface aquifer of the CO₂-rich, cold-water Geyser Andernach (Germany), using ultra-high-resolution mass spectrometry. We detected iGDGT-0, presumably derived from the dominant community member Candidatus Altiarchaeum, providing supporting evidence for its ability to synthesise tetraethers, as previously predicted from metagenomic data. Beyond the typical iGDGT-0 and acyclic glycerol trialkyl glycerol tetraether (iGTGT-0), we discovered novel structural derivatives, here referred to as extended iGDGTs and iGTGTs, characterised by the asymmetrical addition of up to two isoprenoid units to only one of their hydrocarbon side chains, analogous to those found in extended archaeols. The apparent absence of GDGT ring synthase A and B genes in the corresponding metagenome-assembled genome raises the possibility that the producing archaea may utilise extended iGDGTs as a membrane adaptation to cope with the nutrient-depleted conditions of the geyser environment, highlighting the adaptive flexibility of archaea to extreme physicochemical conditions.

The perplexing apusomonads, a sister lineage to Opisthokonta (including animals and fungi), are bacterivorous heterotrophic nanoflagellates whose diversity and ecological role remain poorly understood. Members of the large APU-30 clade are found exclusively in marine environments and mostly comprise uncultured lineages. Here, we isolated a novel lineage within an uncultured subclade of APU-30 from Korean coastal waters. Although the new isolate shares key morphological features with Chelonemonas in APU-30, it possesses a differently segmented dorsal pellicle. Phylogenetic analyses placed this organism closest to the genetically distinct ‘Thecamonas’ sp. Bamfield. Based on a combination of morphological and genetic features, we propose a novel genus and species for this organism: Hexatilemonas jangsaenesis gen. et sp. n. This novel apusomonad captures bacteria with its lateral pseudopodia, showing a sit-and-wait feeding strategy, which probably provides an efficient way for utilising bacterial assemblages. Interestingly, environmental DNA surveys showed a widespread distribution of Hexatilemonas-like sequences across global marine environments, occurring in 29.2% of epipelagic and 47.7% of mesopelagic samples, suggesting that this genus is cosmopolitan. Our findings expand the known diversity of apusomonads by describing a novel lineage and provide insights into previously uncharacterised lineages and their ecological roles in marine ecosystems.

Thermophilic microorganisms, such as those inhabiting hydrothermal environments, play key roles in carbon monoxide (CO) metabolism, thereby influencing global carbon cycling. Members of the genera Thermincola and Carboxydocella are capable of CO oxidation via the water-gas shift reaction, generating H₂, but comprise only two and three validly described species, respectively. In this study, we report the isolation of two novel bacterial strains: strain AZ34E, affiliated with Thermincola, and strain AZ29I, affiliated with Carboxydocella. Comparative genomic and phylogenetic analyses revealed that all currently described isolates within Thermincola and Carboxydocella each represent a single species within their respective genera. Thermincola genomes contain four gene copies encoding [Ni–Fe] CO dehydrogenases, while Carboxydocella genomes harbour six copies with diverse predicted functional roles, suggesting high metabolic flexibility for CO oxidation in these thermophiles. The isolation of the two novel strains, both members of the Bacillota_B phylum, motivated a broader genomic survey across this lineage. This search uncovered numerous candidate organisms with genomic potential for CO oxidation, substantially expanding the diversity of putative carboxydotrophs. These findings highlight the value of targeted genomic mining approaches, which may reveal a much wider array of CO-oxidising microorganisms than currently recognised.

Highbush blueberry (Vaccinium corymbosum L.) fields can remain productive for decades. However, some older fields decline in plant health and exhibit lower yields. After re-planting with new stock, the yields continue to suffer. This condition is termed ‘Replant Disease’. The causative agent(s) in replant disease in New Jersey blueberry fields are unknown. To assess if low- and high-yield blueberry farm soils from two separate farms contained different microbiomes, we coupled long-read bacterial and eukaryotic ribosomal rRNA operon sequencing using the Oxford Nanopore MinION with stable isotope probing (SIP) to detect ¹³C/¹⁵N-utilising soil microbial communities. The results indicate multiple Bacillus species were active on ¹³C/¹⁵N-growth media (predominantly amino acids and glucose) in low-productivity soils from both farms, while high-productivity and adjacent forest soils contained active Burkholderia and Paraburkholderia species. Eukaryotic community profiling indicated Candida blankii, Nadsonia starkeyi and Sugiyamaella chiloensis were slightly enriched and active in low-productivity soils compared with high-productivity soils. This approach differentiates low- and high-productivity blueberry farm soils by ribosomal RNA operon profiling and SIP. The findings also suggest a diagnostic test of blueberry replant affected soils is feasible and may ultimately be used to improve productivity and potentially detect the responsible pathogenic agent(s) or other deleterious microbes.

The nitrous oxide (N₂O) dynamics in boreal forests are better known at the ecosystem scale, with greater uncertainty associated with specific ecosystem compartments. We investigated the N₂O dynamics of the lichen Platismatia glauca in boreal forests near Kuopio, North Savo, Finland. At the study sites, P. glauca is the most abundant lichen colonising Norway spruce (Picea abies). Despite their abundance, the contribution of epiphytic lichens like P. glauca to N₂O dynamics in boreal forests has received little attention. By incubating P. glauca, we assessed the effects of moisture, temperature, and oxygen availability on its N₂O dynamics. We observed net N₂O consumption potential, particularly at +5°C at aerobic condition. Quantitative real-time PCR analysis targeting the N₂O reductase gene fragment (nosZ) revealed that it was present and active in both in situ and incubated lichens. nosZ transcription was higher at +5°C. Clade I nosZ was dominant, with most sequences affiliated with the order Rhizobiales. We confirmed the presence of nosZ gene with targeted metagenomics sequencing. Our results demonstrate that P. glauca acts as a net consumer of N₂O, with potential ranging between 0.1 and 0.4 ng N₂O–N g DW⁻¹ h⁻¹ under aerobic conditions.

Translocating organisms from their natural habitats to laboratories can significantly alter their microbial communities, yet this impact is often overlooked. While common in research, the effects on microbiomes and how laboratory findings relate to natural field dynamics require further study. Symbionts may stabilise microbial communities or increase susceptibility to change, influencing results. This study investigates the effects of laboratory translocation on host-microbiome interactions using the parasitic wasp Asobara japonica and its endosymbiont Wolbachia. Three infected (asexual) and three uninfected (sexual) lines, each with seven iso-female lines, were introduced into the laboratory to track microbial community changes over four generations via 16S rRNA gene sequencing. Our results show laboratory translocation reduces bacterial diversity, with stochastic processes driving changes in the microbial community. Changes in bacterial composition differed between sexual and asexual lines. Over four generations, the asexual wasps' bacterial community became more similar, while sexual wasps exhibited greater diversity. Notably, changes in bacterial communities emerged over generations rather than in the first generation. Finally, Wolbachia abundance varied following laboratory introduction, likely impacting bacterial community structure and assembly over time. Overall, our research highlights how laboratory conditions can affect host-associated microbial communities in different ways, potentially impacting their functions and host interactions.