The degree to which environmental limitations shape the formation and structure of biofilm communities remains a largely unexplored area. The extreme environmental factors in proglacial streams might drive homogenizing selection for biofilm-forming microorganisms. While proglacial streams generally share environmental traits, discrepancies in their environmental characteristics can exert distinct selective forces, leading to nested, spatially organized assembly processes. This study explored bacterial community assembly, focusing on ecologically successful phylogenetic clades in two stream types (glacier-fed mainstems and non-glacier-fed tributaries) across three proglacial floodplains in the Swiss Alps. Throughout all the examined stream types, clades showing low phylogenetic turnover rates, including Gammaproteobacteria and Alphaproteobacteria, were observed. Other clades displayed a stream type-specific distribution. check details In both mainstems and tributaries, the observed community diversity was boosted by these clades, comprising up to 348% and 311% of the total diversity and up to 613% and 509% of the relative abundances, respectively, highlighting their remarkable success. In addition, the proportion of bacteria under homogeneous selective pressure correlated inversely with the amount of photoautotrophs. As a result, these bacterial lineages could experience decreased abundance as proglacial habitats become greener in the future. After all, the impact of distance from the glacier on selected lineages in glacier-fed streams was relatively minor, presumably a consequence of the strong hydrological connection between the studied stream sections. These findings furnish fresh insight into the mechanisms of microbial biofilm construction in proglacial streams, enabling better estimations of their future within a rapidly altering environment. Diverse microbial communities, forming benthic biofilms, are characteristic of streams that drain proglacial floodplains, highlighting their importance. The assembly of microbial communities in high-mountain ecosystems is dynamically responding to climate warming; therefore, a greater understanding of the underlying mechanisms is essential. Within the benthic biofilms of three Swiss Alpine proglacial floodplains, we discovered that homogeneous selection was the primary force in determining the architecture of bacterial communities in glacier-fed main channels and non-glacial tributary streams. However, differences arising from glacier-fed versus tributary ecosystems could entail disparate selective pressures. Proglacial floodplain communities exhibit nested, spatially structured assembly processes, which we discovered here. Our analyses revealed interconnections between aquatic photoautotrophs and bacterial groups under homogenous selection, potentially by providing a readily available source of carbon in these normally carbon-poor ecosystems. The anticipated bacterial community shifts in glacier-fed streams under homogeneous selection are linked to the future rise in the importance of primary production, resulting in a greener stream environment.
Swabbing surfaces within man-made environments to collect microbial pathogens has been a contributing factor to the development of expansive, open-source DNA sequence databases. Digitizing the complex, domain-specific metadata associated with swab site locations is needed for analyzing these data in aggregate through public health surveillance. Currently, the swab site location is captured within a single, free-text field for isolation records, thus generating descriptions that lack precision and standardization. This results from the diverse and irregular phrasing, different levels of detail, and grammatical errors, which obstruct automation efforts and severely reduce machine processing potential. Our assessment encompassed 1498 free-text swab site descriptions, products of routine foodborne pathogen surveillance. An evaluation of the free-text metadata lexicon was undertaken to identify informational facets and the number of unique terms used by data collectors. Using the libraries of the Open Biological Ontologies (OBO) Foundry, hierarchical vocabularies were designed to illustrate swab site locations with logical connections. check details Through content analysis, five distinct facets of information, represented by 338 unique terms, were discovered. Facets of hierarchical terms, alongside statements (dubbed axioms), were developed to delineate the interrelationships between entities within these five domains. A publicly available pathogen metadata standard now incorporates the schema developed during this study, which fosters ongoing surveillance and investigations. NCBI BioSample offered the One Health Enteric Package starting in the year 2022. Employing metadata standards collectively improves the interoperability of DNA sequence databases, enabling extensive data sharing practices, applications of artificial intelligence, and significant advancements in big data solutions for food safety. Public health organizations frequently utilize whole-genome sequence data analysis, particularly from repositories like NCBI's Pathogen Detection Database, to identify and respond to infectious disease outbreaks. Although, metadata located in these databases is commonly deficient and of substandard quality. For use in aggregate analyses, these complex, raw metadata often necessitate reorganization and manual formatting. Public health organizations are compelled to invest a disproportionate amount of interpretive labor to extract actionable information, owing to the inefficient and lengthy nature of these processes. An internationally applicable vocabulary system enabling accurate descriptions of swab site locations is planned to underpin the future use of open genomic epidemiology networks.
The interaction between expanding populations and a changing climate is expected to intensify the contact of humans with pathogens within tropical coastal waters. We analyzed the microbiological water quality in three rivers that lie within 23 km of each other, impacting a Costa Rican beach, and also in the ocean outside their influence zones, both during the rainy and dry seasons. We used a quantitative microbial risk assessment (QMRA) to evaluate the risk of swimming-related gastroenteritis and determine how much pathogen reduction was needed for safe swimming More than 90% of river samples, but only 13% of ocean samples, failed to meet recreational water quality criteria for enterococci. Microbial observations from river samples were categorized by season and subwatershed using multivariate analysis, in contrast to the ocean samples, which were grouped solely based on subwatershed. River samples demonstrated a modeled median risk from all pathogens, ranging between 0.345 and 0.577, which is ten times higher than the U.S. Environmental Protection Agency (U.S. EPA) benchmark of 0.036 (36 illnesses per 1,000 swimmers). Genogroup I norovirus (NoVGI) was the primary contributor to risk, yet adenoviruses escalated the risk beyond the threshold in the two most densely populated sub-basins. Risk assessment highlighted a notable difference between the dry and rainy seasons, with the dry season exhibiting a significantly elevated risk, largely due to the substantially greater frequency of NoVGI detection (100% versus 41%). The necessary viral log10 reduction for safe swimming conditions varied significantly across subwatersheds and seasons, with the highest reductions required during the dry season (38 to 41 in dry; 27 to 32 in rainy). The QMRA, considering the seasonal and local variations in water quality, sheds light on how hydrology, land use, and environmental conditions interact to affect human health risks in tropical coastal areas, leading to improved beach management. This investigation into sanitary water quality at a Costa Rican beach involved a holistic approach to assessing microbial source tracking (MST) marker genes, pathogens, and sewage indicators. Within tropical zones, these kinds of studies are still rare. A quantitative microbial risk assessment (QMRA) determined that rivers affecting the beach repeatedly surpassed the U.S. EPA's risk threshold for gastroenteritis, impacting 36 out of every 1,000 swimmers. Compared to many QMRA studies that leverage surrogate organisms or literature-derived estimates, this investigation offers a significant improvement by directly measuring specific pathogens. By assessing the microbial load and calculating the risk of gastrointestinal illness within each river, we were able to detect differences in pathogen concentrations and associated health risks, even though all rivers suffered from severe wastewater contamination and were situated within 25km of each other. check details Previous studies, to our understanding, have not shown this localized variability.
Temperature variations represent a major factor in the continuous environmental changes faced by microbial communities. Considering the global warming crisis and the more straightforward seasonal changes affecting sea-surface temperatures, this aspect is particularly noteworthy. Microbial responses at the cellular level can unveil their adaptable strategies in reaction to environmental transformations. During the growth of a cold-adapted marine bacterium at differing temperatures (15°C and 0°C), this work investigated the mechanisms maintaining metabolic homeostasis. Our assessment encompassed the quantification of central intracellular and extracellular metabolomes in conjunction with transcriptomic modifications under consistent growth parameters. To contextualize a comprehensive genome-scale metabolic reconstruction, this information was used, enabling a systemic understanding of cellular acclimation to varying temperatures. Our research reveals a substantial metabolic resilience at the level of key central metabolites, but this is balanced by a significant transcriptomic reconfiguration impacting hundreds of metabolic genes' expression. The observed overlapping metabolic phenotypes are a consequence of transcriptomic buffering of cellular metabolism, which enables it to operate despite the wide temperature range.