Environmental Microbiology Reports最新文献

Cacao and coffee are the most economically important crops in the Amazonas region, Peru. Thus, characterising microbial species composition and functional profiles in these rhizospheric soils will enable a comprehensive representation of the metabolic potential of host plants in soils. Accordingly, rhizospheric soil from cacao and coffee farms was collected for both physicochemical and molecular analyses. The diversity and functional roles of the archaeal, bacterial and fungal communities were investigated through a comprehensive DNA metabarcoding analysis. It was found that each crop hosts distinct microbiomes, with a minimal shared core microbiota, underscoring the plant host's role as a primary filter. However, the assembly rules and functional responses diverged significantly across domains. Bacterial communities were compositionally and functionally homogeneous within each crop, shaped by deterministic factors. In contrast, archaeal and fungal compositions were heterogeneous but maintained stable functional profiles within their crop environment. Functionally, prokaryotes (bacteria and archaea) acted as “specialists,” exhibiting significant metabolic divergence between crops. Conversely, fungi served as “generalists,” showing no significant difference in guilds and providing a stable, redundant backbone for decomposition. This tiered microbial response highlights a fundamental ecological dichotomy and underscores the necessity of a multi-kingdom perspective to fully understand and manage the rhizosphere ecosystem.

Host production of nitric oxide in response to P. aeruginosa results in accumulation of nitrite and nitrate at the infection site, with both utilised for anaerobic respiration to support survival. Nitric oxide and nitrite also act as aerobic respiratory inhibitors. P. aeruginosa must overcome these toxic metabolites alongside self-produced cyanide to persist at the infection site. We previously identified a novel nitrite reductase (NirA) that supports P. aeruginosa virulence in a wide range of infection models. In this work, we demonstrate that mutation of nirA inhibits growth of P. aeruginosa at reduced oxygen tensions in the presence of nitrite or nitrate, with this phenotype shown to be dependent on cyanide. NirA is a siroheme-dependent enzyme, a classical target for inhibition with cyanide. Biochemical characterisation confirms that NirA is a novel cyanide-tolerant nitrite reductase, which supports reduction of nitrite in the presence of cyanide. We hypothesise that NirA enables detoxification of nitrite to prevent build-up of multiple respiratory inhibitors and facilitate cyanide-resistant aerobic respiration at low oxygen tensions. Through targeting effectors of these resistance mechanisms, we could promote P. aeruginosa self-poisoning and prevent adaptation to the reduced oxygen environment typically encountered by P. aeruginosa in biofilms and during infection.

This study aimed to analyse the enteric pathogenic bacteria, in fish, soil, and water collected from Kaptai Lake that could be transmitted to humans through handling and consumption. Various types of selective agar media were used to isolate Escherichia coli, Salmonella, Shigella, Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus. After observing the culture morphology, microscopic examination, and biochemical tests were performed. Total plate count indicated varying levels of bacterial load among 20 fish species, Puntius ticto exhibiting the highest (8.53 ± 0.21 × 10⁶ CFU/g) microbial load. Among the soil and water samples, Guccha gram (in Baghaichari) exhibited the highest bacterial load (6.13 ± 0.66 × 10⁶ CFU/g and 3.90 ± 0.20 × 10⁶ CFU/mL, respectively). E. coli in most water and soil samples suggested potential contamination by human and animal faecal matter. Bacterial risk indices showed that 13 fish species among 20 fish samples were categorised as ‘Good’, indicating safe for consumption, and the remaining 7 fish species were identified as ‘Acceptable’. The correlation matrix showed high correlation scores in most places (from 0.5 to 1), indicating that environmental hygiene matters most for the safety of fish. Higher microbial load in soil, water and fish samples emphasises the necessity for strict adherence to reduce zoonotic diseases.

Freshwater ecosystems are under significant environmental stress due to warming and plastic pollution. However, our understanding of their combined effects on primary producers is scarce. We investigated the effects of plain spherical polymethylmethacrylate (PMMA) nanoparticles (NPs) and the acute temperature increases on the growth and fatty acid content of the freshwater green algae Pseudokirchneriella sp. over a 5-day exposure period. The experiment was conducted at three NP concentrations (0.05, 0.5, and 5 mg/L) and two temperature levels (20°C and 25°C). We analysed algal organic matter (AOM) produced during the experiments. Higher temperature stimulated cell growth at lower NP concentrations, but not at the highest NP concentration. Fatty acid composition was affected by temperature but not by NPs. At 20°C, the fractions of low, intermediate, and high molecular weight (MW) AOM had a higher tryptophan-like fluorescence, pointing to a higher protein-like content. Humic-like fluorescence of low MW AOM fractions was higher at higher temperature. At 25°C, the fluorescence response increased slightly with increasing NP concentrations. The findings suggest that temperature has a greater effect on altering fatty acid composition and AOM chemistry than NPs.

The McMurdo Dry Valleys (MDVs) of Antarctica are a uniquely pristine, low-biodiversity model system for understanding fundamental ecological phenomena, the impact of a warming climate on ecosystem functioning, community structure and composition and the dynamics of adaptation. Despite the scientific value of this system, we still know little about the functional ecology of its biota, especially the bacteria. Here, we analysed the bacterial taxonomic and functional diversity of 18 shotgun metagenomes using the VEBA metagenome processing pipeline. We recovered 701 medium-to-high quality metagenome-assembled genomes (MAGs) (≥ 50% completeness and contamination < 10%) and 201 high-quality MAGs (≥ 80% completeness and < 10% contamination), almost 50% more than found in similar sites previously. We found that: (1) community composition shifts along environmental gradients correlated with soil moisture, elevation and distance to the coast; (2) many MDV bacteria are capable of performing trace gas metabolism; (3) genes associated with antibiotic-mediated competitive interactions (e.g., antibiotic biosynthesis and antibiotic resistance genes) are widespread; and (4) MDV bacteria employ survival strategies common to bacteria in similarly extreme environments. This study provides novel insight into microbial survival strategies in extreme environments and lays the groundwork for a more comprehensive understanding of the autecology of MDV bacteria.

Sauerkraut and fermented cucumbers are the most commonly consumed fermented vegetables in several regions of Eastern, Central, and Western Europe; thus, their quality is of great importance. In this study, the quality and bacterial microbiota of commercial samples of fermented cucumbers and sauerkraut were assessed. The identification and quantification of the microbial consortia were performed using nanopore sequencing, and ultrahigh-performance liquid chromatography-tandem mass spectrometry was used to analyse the content of biogenic amines. The physicochemical analysis showed great sample differentiation. Microbial analysis revealed a large diversity of types and relative abundances amongst the studied samples. Lactobacillaceae dominated the microbial community of fermented products, with the most common genera being Latilactobacillus, Leuconostoc, Lactiplantibacillus, Levilactobacillus, Lentilactobacillus, Secundilactobacillus, and Pediococcus. As for biogenic amines, putrescine prevailed both in the samples of fermented cucumber and sauerkraut, followed by cadaverine. The calculated biogenic amine index for four samples of sauerkraut and one of pickled cucumbers exceeded the estimated upper toxicity limit, ranging from 392 to 541, respectively. Spearman correlation analysis showed a significant positive correlation between Secundilactobacillus and cadaverine content in sauerkraut samples and between Levilactobacillus and Secundilactobacillus and cadaverine and histamine content in fermented cucumbers.

Copper bioleaching is a green technology for the recovery of copper from chalcopyrite (CuFeS₂) and chalcocite (Cu₂S) ores. Much remains to be learned about how mineral type and surface chemistry influence microbial community composition. Here, we established a microbial consortium from a copper bioleaching column in Cyprus on chalcopyrite and then sub-cultured it to chalcocite to investigate how the community composition shifts due to changes in mineral structure and the absence of mineral-derived Fe. The solution chemistry was determined and microbial communities characterised by genome-resolved metagenomics after 4 and 8 weeks of cultivation. Acidithiobacillus species and strains, a Rhodospirilales, Leptospirillum ferrodiazotrophum and Thermoplasmatales archaea dominated all enrichments, and trends in abundance patterns were observed with mineralogy and surface-attached versus planktonic conditions. Many bacteria had associated plasmids, some of which encoded metal resistance pathways, sulphur metabolic capacities and CRISPR-Cas loci. CRISPR spacers on an Acidithiobacillus plasmid targeted plasmid-borne conjugal transfer genes found in the same genus, likely belonging to another plasmid, evidence of intra-plasmid competition. We conclude that the structure and composition of metal sulphide minerals select for distinct consortia and associated mobile elements, some of which have the potential to impact microbial activity during sulphide ore dissolution.

Microbial communities in the deep basaltic aquifers of Iceland remain poorly characterized, despite their relevance for understanding subsurface biogeochemical processes, including silicate weathering. Here, we used 16S rRNA gene metabarcoding to investigate bacterial and archaeal diversity in 22 geothermal wells spanning broad gradients in temperature (30°C–110°C), pH (7.0–11.0), and bedrock age (0.01–15 Myr). We observed highly variable microbial assemblages, with several dominant taxa affiliated with known deep biosphere lineages, including hydrogenotrophs and sulfate reducers. Archaeal communities were less diverse and displayed domain-specific patterns, distinct from bacterial assemblages. Beta diversity was primarily structured by temperature and pH, and, to a lesser extent, by bedrock age. Thermodynamic and kinetic parameters derived from groundwater chemistry—including redox potential and silicate dissolution rates—also accounted for significant fractions of the variation in microbial beta diversity, although it cannot be ruled out that their influence primarily reflected underlying correlations with temperature and pH. Our results suggest that both environmental gradients and host-rock reactivity shape microbial diversity in these systems. This highlights the importance of considering geochemical context when designing subsurface microcosm experiments, and identifies candidate taxa for future studies exploring links between microbial composition and silicate weathering processes.

The maintenance and manipulation of the beneficial plant microbiome is a new frontier in ecofriendly disease management, particularly during post-harvest storage. However, the fruit microbiome is highly variable and can be influenced by both biotic and abiotic factors. A comprehensive understanding of how these factors influence microbial communities is necessary in order to unlock the microbiome for sustainable disease management. In this study, we demonstrate the impacts of the growing season and management strategy on the composition and structure of the bacterial microbiome of ‘Honeycrisp’ apples at harvest from seven different orchards in the Atlantic Maritime Ecozone, over the course of two growing seasons. We show that the bacterial communities associated with core and peel tissues respond differently to changes in external environmental conditions, underscoring the need to include multiple tissue types in future fruit microbiome research. Finally, we characterize the microbial cooperation networks of apple core and peel tissues and identify key microbial taxa influencing these networks.

Climate change poses significant challenges to forest ecosystems, particularly influencing processes such as deadwood decomposition and carbon sequestration. This study explores the impact of decaying spruce wood on soil properties, enzymatic activity and microbial structure across an altitudinal gradient in mountain ecosystems dominated by spruce monocultures. In the Babia Góra Massif (Poland), we analysed soils beneath highly decomposed spruce logs (600–1200 m a.s.l.), focusing on soil chemistry, enzymatic activity and microbial composition. Decaying wood enriches soil with carbon and nitrogen, boosting β-glucosidase and phosphatase activities. Increased soil moisture content under decaying wood promotes decomposition and microbial activity. Interestingly, microbial community composition under deadwood exhibited biodiversity changes compared to control soils, and metabolic activity was notably higher, suggesting shifts in microbial function rather than community diversity. The study highlights the significant role of decaying spruce wood in shaping soil properties and microbial processes in mountain ecosystems, emphasising its contribution to carbon and nitrogen enrichment and enhanced enzymatic activities. These findings underscore the ecological importance of deadwood in forest ecosystems, particularly in the context of carbon cycling and climate change adaptation. Sustainable forest management practices should prioritise the retention of deadwood to maintain vital ecosystem functions, particularly in the context of global climate change. Future studies should broaden this approach by including different tree species and additional environmental factors, in order to better understand the variability and resilience of deadwood-driven soil processes across forest ecosystems.