Environmental microbiology最新文献

Long-term ocean warming impacts the marine environment, and these effects will be exacerbated by future climate change affecting, e.g., biogeochemical processes and microbial communities. However, how the sediment microbial cell abundance and live/dead ratio respond to warming is poorly understood. In this study, sediment core samples were collected from a Baltic Sea bay artificially heated on average 5°C for > 50 years above a nearby (control) bay unaffected by the heating. Contrary to the expected increased productivity in the heated bay, qPCR-based sediment cell abundances showed decreased cell numbers along the sediment depth gradient in the heated bay compared to the control bay. This could reflect that a portion of the cells' metabolic energy was diverted to a heat related stress response rather than being used for replication. In addition, live/dead cell ratios showed no clear differences in either bay suggesting the majority of the cells were alive. Finally, sediment depth gradient 16S rRNA gene sequencing confirmed previous studies, showing that prolonged warming shallows sediment biogeochemical zones and related microbial communities. In conclusion, future climate change related warming will likely decrease microbial cell abundances that form part of the food web base, potentially impacting the entire ecosystem.

Thermophilic archaea synthesise cellular membranes composed primarily of isoprenoid glycerol dibiphytanyl glycerol tetraethers (iGDGTs). Cells can adjust the packing of their lipids by increasing cyclopentyl ring production, thereby decreasing membrane permeability and fluidity to maintain cellular function at high temperature, acidic pH, or nutrient limitation. Archaea of the class Nitrososphaeria synthesise crenarchaeol, an iGDGT with four cyclopentyl rings and a cyclohexyl ring, the function of which is unknown. Structural modelling suggests the cyclohexyl ring may increase membrane fluidity, potentially optimising membranes for mesophilic conditions. To investigate the role of crenarchaeol in archaeal membranes in natural settings, we quantify iGDGT compositions of forty-one thermal springs in Yellowstone National Park (YNP), USA, and contextualise these within a global compilation of thermal spring iGDGTs spanning pH values of 1.1–10.1 and temperatures of 16°C–95°C. Spring pH is the strongest predictor of both crenarchaeol relative abundance and the number of cyclopentyl rings per iGDGT. Crenarchaeol relative abundance exhibits a nonlinear relationship with pH and temperature, with highest relative abundances at pH 7.4 and 46°C, decreasing above and below these values. These observations indicate that the cyclohexyl ring of crenarchaeol optimises archaeal cellular membranes for circumneutral and moderate temperature environmental conditions.

This study provides the first clear evidence that edible mushrooms, such as Lentinula edodes (shiitake), Pleurotus ostreatus and Pleurotus eryngii, can generate carbon monoxide (CO) as part of their metabolic activity—independent of bacteria, illumination or oxygen limitation. Systematic measurements of CO and CO₂ emissions were performed over 60 days using multiple fungal species, substrates and growth conditions. Microscopy observations (light, scanning and transmission electron microscopy) confirmed no extracellular and intracellular bacterial endosymbionts involved, supporting a fungal genesis of CO. CO emission patterns showed a parabola-shaped curve, correlating with CO₂ levels regardless measurements by gas-analyser or GC–MS and peaking during full mycelial colonisation. Shiitake mushrooms grown on birch substrate released the highest CO compared to alder and aspen substrates and P. ostreatus and P. eryngii. These findings suggest that fungal respiration contributes to CO dynamics more than previously recognised and highlight the need for further research into its mechanisms and environmental and occupational health implications.

Protists and bacteriophages exert top-down control on bacterial populations. Previous work in the coastal Antarctic demonstrates the potential for intra-seasonal variability of this top-down control driven by the extreme seasonal contrast in bacterial growth rates. We evaluated whether predators ‘kill the winner’ wherein protists and phages preferentially impact the most abundant members of bacterial assemblages over an austral summer with weekly dilution experiments. Seawater from 10 m was divided into two serial dilutions with either 0.2 μm (to evaluate protist grazing) or 30 kDa (to evaluate protist grazing and lysis from bacteriophage) filtered water. We observed strong intra-seasonal change of bacteriophage and protistan contributions to mortality. A comparison of activity per ASV from amplicon sequencing over our dilution experiments to a predicted minimal doubling time indicates that ‘kill the winner’ is occurring during the top-down control of only a few bacteria. As not all bacterial taxa with a predicted low mean doubling time demonstrated high activity in our dilution experiments, our results indicate protists and phage selectively target some fast-growing or abundant bacteria which we term ‘kill select winners’ (KsW). Overall, our evaluation of bacterial abundance and community structure provides unprecedented knowledge of top-down control of marine bacteria.

Salmonella enterica is a major global foodborne pathogen whose success across environmental, agricultural and host-associated niches is closely linked to its ability to form biofilms. Importantly, biofilm formation capacity varies substantially among S. enterica serovars, with broad-host-range serovars such as Salmonella typhimurium and Salmonella enteritidis typically exhibiting robust curli- and cellulose-based biofilms, while host-restricted serovars and recently evolved invasive lineages may display reduced or altered biofilm phenotypes. In this review, we synthesise current knowledge on the molecular regulation, ecological significance and public health impact of biofilm formation in S. enterica, with particular emphasis on conserved CsgD-mediated regulatory pathways characterised in strong biofilm-forming serovars. We describe how biofilm development is controlled by interconnected networks involving CsgD, cyclic-di-GMP signalling and environmental sensing systems. Biofilm growth enhances tolerance to environmental stress, disinfectants, antimicrobials and host immune defenses, facilitating long-term persistence on food-processing surfaces, in agricultural environments and within host niches such as the gallbladder. We further discuss emerging antibiofilm strategies, including matrix-degrading enzymes, quorum-sensing inhibitors, bacteriophages and nanotechnology-based approaches. By integrating molecular mechanisms with ecological and serovar-specific perspectives, this review highlights biofilms as a central adaptive strategy of S. enterica and a critical challenge for food safety and public health.

Karstic aquifers are particularly vulnerable to contaminations but, unlike surface waters, biological indicators of their groundwater quality are lacking. We propose a methodology based on microbial biofilms developed on artificial substrates (clay beads) to evaluate groundwater quality. Clay beads were incubated every 2 months over 18 months in three karstic stations characterised by contrasting nutrient and organic matter inputs from their catchments. After every 2-month incubation, microbial biofilms on clay beads were analysed for biomass, hydrolytic and dehydrogenase activities, and prokaryotic community structure. NH₄⁺, NO₃⁻, PO₄³⁻ and dissolved organic carbon (DOC) concentrations were also measured in groundwater during the experiment. Biofilm biomass and activities were not positively correlated with nutrient and DOC concentrations in groundwater probably due to biofilm growth inhibition by antibiotics in the station having the highest nutrient and DOC concentrations. In contrast, the diversity of prokaryotes in biofilms was positively correlated with nutrient and DOC availability. In the studied heterotrophic karstic stations, the quantity of resources originating from the catchments determined the diversity but also the prokaryotic community structures of biofilms. We selected several microbial taxa as potential indicators of groundwater quality. The next step will be to test their applicability in other karstic ecosystems.

Coral black band disease (BBD) is characterised as a cyanobacteria-dominated microbial mat that rapidly kills underlying coral tissue. Solar radiation promotes lesion progression by fuelling the cyanobacterial photosynthesis, while sulphate-reducing bacteria and sulphide-oxidising bacteria are implicated in sulphide dynamics within the mat. How the metabolism of the key microbial communities in the mat varies under light and dark conditions and impacts lesion virulence is poorly characterised, however. To compare microbial gene expression under different light regimes, we recovered 28 near-complete BBD-derived metagenome-assembled genomes (MAGs) using Oxford Nanopore Technologies long-read sequencing and profiled Illumina metatranscriptomic reads from BBD lesions collected at day and night by mapping to these MAGs. Genes from the cyanobacterium Roseofilum reptotaenium dominated the differentially expressed genes, with photosynthesis highly represented during the daytime. Relative expression of sulphur and nitrogen metabolism, cofactor biosynthesis, chemotaxis and motility increased among the non-cyanobacterial members at night. Enhanced sulphur reduction by Campylobacteriales and Desulfovibrionaceae at night likely supports a sulphide-rich and low oxygen micro-environment in the lesion, while increased chemotaxis and motility by Campylobacteriales and other heterotrophic bacteria drive lesion progression towards healthy coral tissue. This study provides insights into how diurnal light dynamics drive microbial metabolic pathways changes, thereby promoting BBD virulence.

Black soldier fly larvae (BSFL) are increasingly valued as a sustainable protein source for aquaculture and can be reared on local industrial side streams, enhancing their environmental and economic benefits. The resulting frass—a byproduct of larval excreta and residual feed—shows promise as an organic fertiliser. In addition to its nutrient content, frass contains microbial communities that may enhance plant growth through phytohormone production, nitrogen fixation, and organic matter turnover. Yet, the roles of feed composition and thermal hygienisation in shaping these communities remain underexplored. This study examined the impact of five feed substrates, including industrial side streams and a control diet, on frass microbial composition, and assessed responses to thermal treatment. Feed nutrients were characterised, and microbial communities profiled using amplicon sequencing. Viable populations were quantified via culture-based methods, with bacterial isolates taxonomically classified. Feed type was the dominant factor influencing frass microbiota, with distinct communities reflecting substrate nutritional profiles. High-fibre diets promoted fungal diversity and abundance, while high-protein feeds enriched specific bacterial taxa. Thermal hygienisation had a heterogeneous effect on viable counts but minimal impact on overall community structure. These findings support microbiome-informed feed design to tailor frass microbial profiles for enhanced biofertiliser function in sustainable agriculture.