Applied and Environmental Microbiology最新文献

Co-evolution of bacterial defense systems and phage counter-defense mechanisms has resulted in an intricate biological interplay between bacteriophages and their prey. In order to evade nuclease-based mechanisms that target DNA, various bacteriophages modify their nucleobases, which impedes or even inhibits the recognition and restriction by endonucleases. We found that Shewanella phage Thanatos DNA is insensitive to multiple restriction enzymes and also to Cas I-Fv and Cas9 cleavage. Furthermore, with nanopore sequencing, the phage DNA showed severely impaired basecalling. In addition to an adenine methylation, the data indicated an additional, much more substantial nucleobase modification. Using liquid chromatography-mass spectrometry (LC-MS), we identified an unknown configuration of a deoxypentose attached to cytosine as an undiscovered modification of phage DNA, which is present in Thanatos genomic DNA and likely mediates resistance to restriction endonucleases, as well as reducing Cas nuclease activity significantly. To elucidate the underlying enzyme functions, we identified structural homologs of Thanatos proteins among known glycosyltransferase folds and experimentally proved a UDP-xylose pyrophosphorylase function of the phage protein TH1_063 by in vitro. Inactivation of TH1_060 leads to an almost complete inhibition of phage propagation, indicating an important role of the cytosine modification in phage survival and/or proliferation.

Importance: Several phages extensively decorate their DNA building blocks, providing an effective protection against various host and phage-produced restriction systems. These modifications allow the phages to distinguish between their own DNA and that of the host, significantly increasing the establishment of the phage chromosome upon entry into the host and subsequent phage proliferation. Several different modifications have been previously identified and characterized. Here, we describe a hitherto unknown cytosine modification, consisting of a deoxypentose-putatively xylose-that provides protection against various bacterial restriction systems, including DNA-targeting CRISPR/Cas systems. Our findings expand the range of DNA modifications that phages use for protection.

A consequence of past acid rain events has been chronic acidification of Nova Scotian forests, leading to a loss of essential nutrients and subsequent decreases in forest productivity and biodiversity. Liming-supplementing forests with crushed limestone-can restore essential nutrients to acidified soils and increase the pH of soils and the carbon capture by forests through the promotion of tree growth. Liming treatments are often assessed through tree growth measurements, although little is known about how microorganisms respond to these changes in pH and nutrient availability. Understanding the impacts of liming on microbial communities will help determine whether liming is a good remediation strategy for Nova Scotia. A pilot study evaluating liming in acidified forests in Nova Scotia began in 2017. Microbiome analysis (prokaryotic 16S and fungal ITS2 rRNA gene amplicon sequencing) of three different horizons (depths; upper forest floor, lower forest floor, and upper B horizon) of soil in a softwood forest area showed significant differences between lime-treated and control soils for the prokaryotic but not fungal communities, particularly in the uppermost soil horizon. Several genera from the Alphaproteobacteria class were significantly higher in abundance in treated than control soils, whereas genera from the Acidobacteriia (previously Acidobacteriae) class were significantly lower in abundance in treated versus control soils. Soil chemistry analysis of the same three horizons showed a significant increase in base cations and pH of the uppermost soil horizon in control versus treatment sites.IMPORTANCEForests are increasingly being managed with an emphasis on understanding how forests function. Lime amendments are used to promote forest health and increase resilience to climate change. To date, only a handful of studies have analyzed the effects of liming on microbial communities in forest soils. Our study combines soil chemistry with prokaryotic and fungal communities of limed and control soils. Shifts in microbial composition that are coincident with liming may provide early indications of the effectiveness of liming and provide insight into the roles of microbes in forest health.

The surface soil horizon, functioning as the biogeochemical nexus in paddy ecosystems, harbors architecturally complex microbial consortia where abundant and rare taxa exhibit functional redundancy. While these aggregates drive critical nutrient cycling processes, the mechanistic partitioning of ecological roles between abundant and rare subcommunities remains obscured, limiting the development of microbiota-targeted agricultural optimization strategies. To experimentally dissect their functional hierarchies, we developed a controlled culturing system (26°C, 12 h light-dark cycle, 10,000-12,000 lux; nutrient supply: 10% soil leachate + 0.5% mineral solution) to selectively suppress rare taxa while preserving the abundant taxa. Systematic functional partitioning revealed three cardinal determinants of abundant subcommunity ecological predominance: abundant taxa (i) account for >50% of the microbial diversity; (ii) dominate community assembly processes; and (iii) exert greater influence on carbon, nitrogen, and sulfur cycling compared to rare taxa. Our approach establishes causal relationships beyond bioinformatic speculation, providing a functional disentanglement framework that redefines abundant taxa as keystone engineers of aggregate stability and functionality. This conceptual shift holds significant promise for the advancement of precision agriculture and the development of more sustainable nutrient management approaches.IMPORTANCEMoving beyond traditional approaches to bioinformation analysis, this study employed an experimental strategy featuring a novel microbial filtration system. This system was designed to selectively remove rare species, thereby enabling the identification of the predominant roles played by abundant species within microbial aggregates. The findings demonstrate that abundant species are critical for maintaining community stability, governing assembly processes, and exerting greater ecological functions. Beyond introducing a filtration technique capable of distinguishing abundant and rare species in periphyton-like microbial communities, this work provides experimental evidence supporting the prioritization of abundant species in future efforts aimed at regulating periphyton growth or developing periphyton-based biotechnologies for nutrient cycling optimization.

English has become the global language of science, but this dominance has a cost. Researchers who are not native English speakers face invisible hurdles: efforts to learn and use a second language, obstacles to research dissemination, and diminished professional visibility. These barriers do more than prevent access to opportunities. They cement unfair assumptions about scientific competence and preferentially amplify voices that are proficient, or perceived to be proficient, in the dominant language, shaping scientific discourse in narrow and exclusive ways. This editorial explores how linguistic bias sustains professional hierarchies and restricts scientific progress. It also highlights our journal's initiatives to overcome language-based barriers in publishing and foster equitable participation in scientific exchange.

Nitric oxide (NO) is an important biological signaling molecule. S-nitrosoglutathione reductase (GSNOR), a master regulator of NO signaling, regulates various biological processes. However, little is known about the role of GSNOR in Aspergillus flavus. Here, we identified a gene encoding GSNOR in this aflatoxigenic fungus and demonstrated that GSNOR shows activity during the critical life cycle stages, including spore germination, hyphal growth, and conidiogenesis. We found that GSNOR plays a crucial role in NO homeostasis, as GSNOR deletion resulted in significantly elevated NO levels and heightened sensitivity to exogenous NO stress. GSNOR also participated in multiple biological processes in A. flavus; for that, GSNOR deletion impaired conidia germination, reduced growth, decreased conidiogenesis and sclerotial development, attenuated virulence on kernels, and notably decreased aflatoxin production. Furthermore, we demonstrated that GSNOR is important for reactive oxygen species (ROS) balance, as its deletion significantly elevated mycelial ROS levels and made the strain more sensitive to oxidative stress.IMPORTANCEAspergillus flavus is a notorious saprophytic filamentous fungus, with its production of carcinogenic aflatoxins posing serious threats to food safety and human health. Aflatoxin contamination prevention and control have long been a global challenge. In previous studies, we observed that nitric oxide (NO) significantly inhibits the aflatoxin production by A. flavus. This study further investigated the role of the key regulatory enzyme S-nitrosoglutathione reductase (GSNOR) in the NO signaling pathway. Our findings indicate that GSNOR is crucial for maintaining both NO homeostasis and reactive oxygen species (ROS) balance and plays an essential role in fungal development, pathogenicity, and aflatoxin biosynthesis. These results highlight the potential of targeting components in the NO signaling pathway, such as GSNOR, as a novel strategy for the early prevention of aflatoxin contamination in food.

Antimicrobial resistance is one of the largest and most pressing global health threats. This is not only a huge burden on the global economy but also a growing threat to animal, environmental, plant, and human health, and new strategies are needed to avoid resistance and improve treatment. Novel antimicrobial resistance genes are normally first detected once they cause problems in clinical infections, and we have limited knowledge on their evolutionary trajectories. Current antimicrobial susceptibility testing and research have a limited focus on key environmental factors in pathogen-reservoir-host interactions, possibly leading to inaccurate results that do not reflect the in vivo conditions. Focusing on differences in pH, we determined the MIC of a panel of isogenic strains expressing CTX-M-15 and CMY-2 β-lactamases. We found that pH has a large impact on the activity of β-lactamases, and treatment of these resistant isolates could be possible if the pH of the environment is modified. We verified this using enzyme kinetics, co-cultures, and growth experiments, suggesting that exposure to different environmental conditions may lead to distinct evolutionary trajectories for specific β-lactamases. Exploring the effect of different temperatures, we also observed a differential effect of avian and mammal host temperatures. Environmental factors such as pH and temperature may have a large unnoticed effect on antimicrobial resistance, and we might use this knowledge to renew and extend the use of old antibiotics for certain infections.IMPORTANCEAntimicrobial resistance is a huge burden to global health and economy. We need new options for avoiding selection of resistance and improved treatment. Overlooked aspect: current susceptibility testing does not take pH into account. With this study, we show that pH and temperature can have large and contrasting effects on the activity (and therefore MIC) of specific β-lactamases. This might help to explain the phenomenon of bacteria often harboring multiple β-lactamases seemingly with the same function as well as be utilized to enable treatment of genotypically resistant strains under very specific conditions, that is, treatment of CTX-M-15, the most prevalent ESBL in healthcare, under alkaline conditions.

The steady state of gut microbiota is a key factor in regulating the growth of broilers. The regulatory role of wet-fermented brewer's grain (WFBG) in broiler gut development and microbiota is still elusive. In this study, non-targeted metabolomics and 16S rRNA sequencing analysis were used to investigate the effects of WFBG supplementation on serum metabolites and gut microbiota in 42-day-old broilers. Serum metabolomic analysis identified 546 differentially expressed metabolites (DEMs), with GO and KEGG enrichment analyses showing that specific DEMs were enriched in intestinal development-related pathways, including phenylalanine, tyrosine, tryptophan biosynthesis, and alpha-linolenic acid metabolism. 16S rRNA sequencing analysis showed significant intergroup differences in the relative abundances of Ligilactobacillus, Olsenella, Erysipelatoclostridium, and Blautia at the genus level in broiler gut microbiota between the control and WFBG groups. Integrative analysis of 16S rRNA sequencing and non-targeted metabolomics demonstrated that bacterial genera, including Streptococcus and Proteus, were positively correlated with N6,N6-dimethyllysine and quercetin but negatively associated with 18 DEMs, such as 4-methylbenzenesulfonic acid and deoxycholic acid derivatives. Furthermore, we identified potential biomarkers associated with intestinal development induced by 20% WFBG supplementation. Our findings suggest that the maximum recommended inclusion level of WFBG in broiler feed should not exceed 20%. This study provides novel insights into the molecular mechanisms underlying fiber utilization and intestinal maturation in broilers.

Importance: This study investigated the regulatory mechanism of wet-fermented brewer's grain (WFBG) on gut development and microbiota in commercial broilers. Through integrated 16S rRNA sequencing and non-targeted metabolomic analysis, the study not only identified differential gut microbiota, serum metabolites, as well as their correlations, but also discovered potential biomarkers associated with intestinal development induced by 20% WFBG and clarified the maximum recommended inclusion level of WFBG (≤20%). This not only filled the gap in the molecular mechanism underlying WFBG-mediated regulation of fiber utilization and intestinal maturation in broilers but also provided a theoretical basis and practical guidance for the resource utilization of agricultural by-products, precision feeding of broilers, and intestinal health monitoring.

In polymicrobial communities, microorganisms do not exist in isolation but engage in complex and dynamic interactions. Emerging evidence indicates that these microbial interactions can profoundly influence key aspects of antibiotic action, including antibiotic activity and the emergence and dissemination of antibiotic resistance. This mini-review examines the mechanistic pathways through which intra- and inter-specific interactions facilitate both individual and community-level responses to antibiotic treatment. Such interactions can also reshape the selective pressures imposed by antibiotics, thereby altering evolutionary trajectories toward resistance. We emphasize the importance of considering the ecological context of microbial communities as essential for advancing our understanding of antibiotic resistance and for developing more effective and sustainable antibiotic strategies.

Exposures to both human and animal feces pose human health risks, particularly for young children in low- and middle-income country (LMIC) settings where domestic animals are common, water and sanitation infrastructure is often limited, and enteropathogen transmission is high. Microbial source tracking (MST) markers specific to feces from humans and particular animal types can be used to identify the provenance of microbial contamination, yet most MST studies explore few household environmental sample types, limiting the understanding of how marker utility varies by matrix. We validated qPCR assays for six MST markers and quantified their prevalence in 585 samples from 59 households spanning an urban-rural gradient in northwestern Ecuador. We used GenBac3 to test for general fecal contamination and HF183, Rum2Bac, Pig2Bac, DG37, and GFD to test for human, ruminant, swine, dog, and avian contamination, respectively. Approximately 10 sample types were collected per household, including the following: rinses of child and adult hands, swabs of floors and surfaces, soil, domestic and drinking water, and food. GenBac3 and HF183 were detected in 77.82% and 15.36% of samples, respectively. Animal-associated markers were detected less frequently, in 0.5%-4.1% of samples. However, when present, animal marker concentrations were comparable to HF183. Host-associated markers were most often detected in adult and child hand rinse and floor samples, and GenBac3 concentrations were highest in hand rinse samples. HF183 detection on adult caregiver hands was associated with increased odds of HF183 detection on children's hands and floors. Together, these findings identify hands and floors as reservoirs of fecal contamination and highlight the need for integrated interventions that address both human and animal sources to address household exposures to reduce exposures to enteric pathogens.

Importance: Understanding the sources and pathways of detectable household environmental fecal contamination is critical for identifying how exposures occur and for developing targeted interventions to reduce risk of enteric infection. By linking contamination on caregiver hands to that on children's hands and floors, we highlight a likely route for pathogen transfer in the home. The inclusion of multiple host-associated markers across a wide range of sample types reveals patterns that narrower studies may miss, offering new insights into the complex ecology of fecal contamination. These findings can inform sampling strategies, guide risk assessments, and support the design of interventions aimed at reducing child exposure to enteric pathogens in similar high-risk settings.