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1. Cast iron drinking water pipe biofilms support diverse microbial communities containing antibiotic resistance genes, metal resistance genes, and class 1 integrons

   https://doi.org/10.1039/D0EW01059F  

   Kimbell, Lee K. ; LaMartina, Emily Lou ; Kappell, Anthony D. ; Huo, Jingwan ; Wang, Yin ; Newton, Ryan J. ; McNamara, Patrick J. ( March 2021 , Environmental Science: Water Research & Technology)

   null (Ed.)

   Antimicrobial resistance is a well-documented public health concern. The role that drinking water distribution pipes have as sources of antibiotic resistance genes (ARGs) is not well known. Metals are a known stressor for antibiotic resistance development, implying that aging metal-pipe infrastructure could be a source of ARGs. The objective of this study was to determine if ARGs, metal resistance genes (MRGs), and intI 1 were pervasive across various pipe biofilm sample types (biomass surfaces, pipe surfaces, corrosion tubercles, and under corrosion tubercles) and if the resistance genes associated with particular microbial taxa. Eight sample types in triplicate ( n = 24) were taken from inside a >100 year-old, six ft. section of a full-scale chloraminated cast iron drinking water main. Droplet digital PCR (ddPCR) was employed as a novel approach to quantify ARGs in pipes from full-scale drinking water distribution systems (DWDS) because it yielded higher detection frequencies than quantitative PCR (qPCR). Illumina sequencing was employed to characterize the microbial community based on 16S rRNA genes. ARGs and MRGs were detected in all 24 pipe samples. Every sample contained targeted genes. Interestingly, the mean absolute abundances of ARGs and MRGs only varied by approximately one log value across sample types, but the mean relative abundances (copy numbers normalized to 16S rRNA genes) varied by over two log values. The ARG and MRGs concentrations were not significantly different between sample types, despite significant changes in dominant microbial taxa. The most abundant genera observed in the biofilm communities were Mycobacterium (0.2–70%), and β-lactam resistance genes bla TEM , bla SHV , and the integrase gene of class 1 integrons ( intI 1) were positively correlated with Mycobacterium . The detection of ARGs, MRGs, and class 1 integrons across all sample types within the pipe indicates that pipes themselves can serve as sources for ARGs in DWDS. Consequently, future work should investigate the role of pipe materials as well as corrosion inhibitors to determine how engineering decisions can mitigate ARGs in drinking water that stem from pipe materials. 

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2. Legionella pneumophila occurrence in drinking water supplied by private wells

   https://doi.org/10.1111/lam.13273  

   Mapili, K. ; Pieper, K. J. ; Dai, D. ; Pruden, A. ; Edwards, M. A. ; Tang, M. ; Rhoads, W. J. ( April 2020 , Letters in Applied Microbiology)

   Unregulated private wells are understudied potential sources of community-acquired Legionnaires’ disease. Here we conducted a comprehensive survey of 44 homes supplied by private wells in Wake County, North Carolina, quantifying Legionella spp. DNA, Legionella pneumophila DNA, and total bacterial 16S rRNA genes via real-time polymerase chain reaction in hot and cold drinking water samples, along with culturable L. pneumophila via IDEXX Legiolert in cold drinking water samples. Legionella spp. DNA, L. pneumophila DNA and culturable L. pneumophila were detected in 100, 65·5 and 15·9% of the 44 homes, respectively, and culturable levels were comparable to some municipal surveys applying the same methods. Total coliforms and Escherichia coli were monitored as representative faecal indicators and were found in 20·4 and 0·0% of homes. Within certain sample types, Legionella spp. and L. pneumophila gene copy numbers were positively associated with total bacteria (i.e. total 16S rRNA genes) and water softener use, but were not associated with faecal indicator bacteria, inorganic water parameters or other well characteristics. These findings confirm that occurrence of Legionella and L. pneumophila is highly variable in private wells.

   Legionella is the leading identified cause of waterborne disease outbreaks associated with US municipal water systems. While Legionella is known to occur naturally in groundwater, prior efforts to characterize its occurrence in unregulated private wells are limited to sampling at the wellhead and not in the home plumbing where Legionella can thrive. This work documents much higher levels of Legionella in home plumbing versus water directly from private wells and examines factors associated with higher Legionella occurrence.

    

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3. Landscape characteristics shape surface soil microbiomes in the Chihuahuan Desert

   https://doi.org/10.3389/fmicb.2023.1135800  

   Hansen, Frederick A. ; James, Darren K. ; Anderson, John P. ; Meredith, Christy S. ; Dominguez, Andrew J. ; Pombubpa, Nuttapon ; Stajich, Jason E. ; Romero-Olivares, Adriana L. ; Salley, Shawn W. ; Pietrasiak, Nicole ( June 2023 , Frontiers in Microbiology)

   Introduction Soil microbial communities, including biological soil crust microbiomes, play key roles in water, carbon and nitrogen cycling, biological weathering, and other nutrient releasing processes of desert ecosystems. However, our knowledge of microbial distribution patterns and ecological drivers is still poor, especially so for the Chihuahuan Desert. Methods This project investigated the effects of trampling disturbance on surface soil microbiomes, explored community composition and structure, and related patterns to abiotic and biotic landscape characteristics within the Chihuahuan Desert biome. Composite soil samples were collected in disturbed and undisturbed areas of 15 long-term ecological research plots in the Jornada Basin, New Mexico. Microbial diversity of cross-domain microbial groups (total Bacteria, Cyanobacteria, Archaea, and Fungi) was obtained via DNA amplicon metabarcode sequencing. Sequence data were related to landscape characteristics including vegetation type, landforms, ecological site and state as well as soil properties including gravel content, soil texture, pH, and electrical conductivity. Results Filamentous Cyanobacteria dominated the photoautotrophic community while Proteobacteria and Actinobacteria dominated among the heterotrophic bacteria. Thaumarchaeota were the most abundant Archaea and drought adapted taxa in Dothideomycetes and Agaricomycetes were most abundant fungi in the soil surface microbiomes. Apart from richness within Archaea ( p  = 0.0124), disturbed samples did not differ from undisturbed samples with respect to alpha diversity and community composition ( p  ≥ 0.05), possibly due to a lack of frequent or impactful disturbance. Vegetation type and landform showed differences in richness of Bacteria, Archaea, and Cyanobacteria but not in Fungi. Richness lacked strong relationships with soil variables. Landscape features including parent material, vegetation type, landform type, and ecological sites and states, exhibited stronger influence on relative abundances and microbial community composition than on alpha diversity, especially for Cyanobacteria and Fungi. Soil texture, moisture, pH, electrical conductivity, lichen cover, and perennial plant biomass correlated strongly with microbial community gradients detected in NMDS ordinations. Discussion Our study provides first comprehensive insights into the relationships between landscape characteristics, associated soil properties, and cross-domain soil microbiomes in the Chihuahuan Desert. Our findings will inform land management and restoration efforts and aid in the understanding of processes such as desertification and state transitioning, which represent urgent ecological and economical challenges in drylands around the world. 

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4. Regional biogeography versus intra-annual dynamics of the root and soil microbiome

   https://doi.org/10.1186/s40793-023-00504-x  

   Bell-Dereske, Lukas P. ; Benucci, Gian Maria Niccolò ; da Costa, Pedro Beschoren ; Bonito, Gregory ; Friesen, Maren L. ; Tiemann, Lisa K. ; Evans, Sarah E. ( June 2023 , Environmental Microbiome)

   Root and soil microbial communities constitute the below-ground plant microbiome, are drivers of nutrient cycling, and affect plant productivity. However, our understanding of their spatiotemporal patterns is confounded by exogenous factors that covary spatially, such as changes in host plant species, climate, and edaphic factors. These spatiotemporal patterns likely differ across microbiome domains (bacteria and fungi) and niches (root vs. soil).

   To capture spatial patterns at a regional scale, we sampled the below-ground microbiome of switchgrass monocultures of five sites spanning > 3 degrees of latitude within the Great Lakes region. To capture temporal patterns, we sampled the below-ground microbiome across the growing season within a single site. We compared the strength of spatiotemporal factors to nitrogen addition determining the major drivers in our perennial cropping system. All microbial communities were most strongly structured by sampling site, though collection date also had strong effects; in contrast, nitrogen addition had little to no effect on communities. Though all microbial communities were found to have significant spatiotemporal patterns, sampling site and collection date better explained bacterial than fungal community structure, which appeared more defined by stochastic processes. Root communities, especially bacterial, were more temporally structured than soil communities which were more spatially structured, both across and within sampling sites. Finally, we characterized a core set of taxa in the switchgrass microbiome that persists across space and time. These core taxa represented < 6% of total species richness but > 27% of relative abundance, with potential nitrogen fixing bacteria and fungal mutualists dominating the root community and saprotrophs dominating the soil community.

   Our results highlight the dynamic variability of plant microbiome composition and assembly across space and time, even within a single variety of a plant species. Root and soil fungal community compositions appeared spatiotemporally paired, while root and soil bacterial communities showed a temporal lag in compositional similarity suggesting active recruitment of soil bacteria into the root niche throughout the growing season. A better understanding of the drivers of these differential responses to space and time may improve our ability to predict microbial community structure and function under novel conditions.

    

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5. Associated bacterial communities, confrontation studies, and comparative genomics reveal important interactions between Morchella with Pseudomonas spp.

   https://doi.org/10.3389/ffunb.2023.1285531  

   Cailleau, Guillaume ; Hanson, Buck T. ; Cravero, Melissa ; Zhioua, Sami ; Hilpish, Patrick ; Ruiz, Celia ; Robinson, Aaron J. ; Kelliher, Julia M. ; Morales, Demosthenes ; Gallegos-Graves, La Verne ; et al ( December 2023 , Frontiers in Fungal Biology)

   Members of the fungal genusMorchellaare widely known for their important ecological roles and significant economic value. In this study, we used amplicon and genome sequencing to characterize bacterial communities associated with sexual fruiting bodies from wild specimens, as well as vegetative mycelium and sclerotia obtained fromMorchellaisolates grownin vitro. These investigations included diverse representatives from both Elata and EsculentaMorchellaclades. Unique bacterial community compositions were observed across the various structures examined, both within and across individualMorchellaisolates or specimens. However, specific bacterial taxa were frequently detected in association with certain structures, providing support for an associated core bacterial community. Bacteria from the genusPseudomonasandRalstoniaconstituted the core bacterial associates ofMorchellamycelia and sclerotia, while other genera (e.g.,Pedobacterspp.,Deviosaspp., andBradyrhizobiumspp.) constituted the core bacterial community of fruiting bodies. Furthermore, the importance ofPseudomonasas a key member of the bacteriome was supported by the isolation of severalPseudomonasstrains from mycelia duringin vitrocultivation. Four of the six mycelial-derivedPseudomonasisolates shared 16S rDNA sequence identity with amplicon sequences recovered directly from the examined fungal structures. Distinct interaction phenotypes (antagonistic or neutral) were observed in confrontation assays between these bacteria and variousMorchellaisolates. Genome sequences obtained from thesePseudomonasisolates revealed intriguing differences in gene content and annotated functions, specifically with respect to toxin-antitoxin systems, cell adhesion, chitinases, and insecticidal toxins. These genetic differences correlated with the interaction phenotypes. This study provides evidence thatPseudomonasspp. are frequently associated withMorchellaand these associations may greatly impact fungal physiology.

    

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