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1. Evaluating the potential of residual Pap test fluid as a resource for the metaproteomic analysis of the cervical-vaginal microbiome

   https://doi.org/10.1038/s41598-018-29092-4  

   Afiuni-Zadeh, Somaieh ; Boylan, Kristin L. M. ; Jagtap, Pratik D. ; Griffin, Timothy J. ; Rudney, Joel D. ; Peterson, Marnie L. ; Skubitz, Amy P. N. ( July 2018 , Scientific Reports)

   The human cervical-vaginal area contains proteins derived from microorganisms that may prevent or predispose women to gynecological conditions. The liquid Pap test fixative is an unexplored resource for analysis of microbial communities and the microbe-host interaction. Previously, we showed that the residual cell-free fixative from discarded Pap tests of healthy women could be used for mass spectrometry (MS) based proteomic identification of cervical-vaginal proteins. In this study, we reprocessed these MS raw data files for metaproteomic analysis to characterize the microbial community composition and function of microbial proteins in the cervical-vaginal region. This was accomplished by developing a customized protein sequence database encompassing microbes likely present in the vagina. High-mass accuracy data were searched against the protein FASTA database using a two-step search method within the Galaxy for proteomics platform. Data was analyzed by MEGAN6 (MetaGenomeAnalyzer) for phylogenetic and functional characterization. We identified over 300 unique peptides from a variety of bacterial phyla andCandida. Peptides corresponding to proteins involved in carbohydrate metabolism, oxidation-reduction, and transport were identified. By identifying microbial peptides in Pap test supernatants it may be possible to acquire a functional signature of these microbes, as well as detect specific proteins associated with cervical health and disease.

    

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2. Radiolytically reworked Archean organic matter in a habitable deep ancient high-temperature brine

   https://doi.org/10.1038/s41467-023-41900-8  

   Nisson, Devan M. ; Walters, Clifford C. ; Chacón-Patiño, Martha L. ; Weisbrod, Chad R. ; Kieft, Thomas L. ; Sherwood Lollar, Barbara ; Warr, Oliver ; Castillo, Julio ; Perl, Scott M. ; Cason, Errol D. ; et al ( October 2023 , Nature Communications)

   Investigations of abiotic and biotic contributions to dissolved organic carbon (DOC) are required to constrain microbial habitability in continental subsurface fluids. Here we investigate a large (101–283 mg C/L) DOC pool in an ancient (>1Ga), high temperature (45–55 °C), low biomass (10²−10⁴cells/mL), and deep (3.2 km) brine from an uranium-enriched South African gold mine. Excitation-emission matrices (EEMs), negative electrospray ionization (–ESI) 21 tesla Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS), and amino acid analyses suggest the brine DOC is primarily radiolytically oxidized kerogen-rich shales or reefs, methane and ethane, with trace amounts of C₃–C₆hydrocarbons and organic sulfides. δ²H and δ¹³C of C₁–C₃hydrocarbons are consistent with abiotic origins. These findings suggest water-rock processes control redox and C cycling, helping support a meagre, slow biosphere over geologic time. A radiolytic-driven, habitable brine may signal similar settings are good targets in the search for life beyond Earth.

    

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3. Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type

   https://doi.org/10.1128/mBio.00416-20  

   Sharrar, Allison M. ; Crits-Christoph, Alexander ; Méheust, Raphaël ; Diamond, Spencer ; Starr, Evan P. ; Banfield, Jillian F. ( June 2020 , mBio)

   Davies, Julian E. (Ed.)

   ABSTRACT Bacteria isolated from soils are major sources of specialized metabolites, including antibiotics and other compounds with clinical value that likely shape interactions among microbial community members and impact biogeochemical cycles. Yet, isolated lineages represent a small fraction of all soil bacterial diversity. It remains unclear how the production of specialized metabolites varies across the phylogenetic diversity of bacterial species in soils and whether the genetic potential for production of these metabolites differs with soil depth and vegetation type within a geographic region. We sampled soils and saprolite from three sites in a northern California Critical Zone Observatory with various vegetation and bedrock characteristics and reconstructed 1,334 metagenome-assembled genomes containing diverse biosynthetic gene clusters (BGCs) for secondary metabolite production. We obtained genomes for prolific producers of secondary metabolites, including novel groups within the Actinobacteria , Chloroflexi , and candidate phylum “ Candidatus Dormibacteraeota.” Surprisingly, one genome of a candidate phyla radiation (CPR) bacterium coded for a ribosomally synthesized linear azole/azoline-containing peptide, a capacity we found in other publicly available CPR bacterial genomes. Overall, bacteria with higher biosynthetic potential were enriched in shallow soils and grassland soils, with patterns of abundance of BGC type varying by taxonomy. IMPORTANCE Microbes produce specialized compounds to compete or communicate with one another and their environment. Some of these compounds, such as antibiotics, are also useful in medicine and biotechnology. Historically, most antibiotics have come from soil bacteria which can be isolated and grown in the lab. Though the vast majority of soil bacteria cannot be isolated, we can extract their genetic information and search it for genes which produce these specialized compounds. These understudied soil bacteria offer a wealth of potential for the discovery of new and important microbial products. Here, we identified the ability to produce these specialized compounds in diverse and novel bacteria in a range of soil environments. This information will be useful to other researchers who wish to isolate certain products. Beyond their use to humans, understanding the distribution and function of microbial products is key to understanding microbial communities and their effects on biogeochemical cycles. 

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4. Bacteriophage-mediated lysis supports robust growth of amino acid auxotrophs

   https://doi.org/10.1038/s41396-023-01452-7  

   Pherribo, Gordon J. ; Taga, Michiko E. ( June 2023 , The ISME Journal)

   Microbial communities host many auxotrophs—organisms unable to synthesize one or more metabolites required for their growth. Auxotrophy is thought to confer an evolutionary advantage, yet auxotrophs must rely on other organisms that produce the metabolites they require. The mechanisms of metabolite provisioning by “producers” remain unknown. In particular, it is unclear how metabolites such as amino acids and cofactors, which are found inside the cell, are released by producers to become available to auxotrophs. Here, we explore metabolite secretion and cell lysis as two distinct possible mechanisms that result in the release of intracellular metabolites from producer cells. We measured the extent to which secretion or lysis of Escherichia coli and Bacteroides thetaiotaomicron amino acid producers can support the growth of engineered Escherichia coli amino acid auxotrophs. We found that cell-free supernatants and mechanically lysed cells provide minimal levels of amino acids to auxotrophs. In contrast, bacteriophage lysates of the same producer bacteria can support as many as 47 auxotroph cells per lysed producer cell. Each phage lysate released distinct levels of different amino acids, suggesting that in a microbial community the collective lysis of many different hosts by multiple phages could contribute to the availability of an array of intracellular metabolites for use by auxotrophs. Based on these results, we speculate that viral lysis could be a dominant mechanism of provisioning of intracellular metabolites that shapes microbial community structure.

    

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5. The role of differential DMSP production and community composition in predicting variability of global surface DMSP concentrations

   https://doi.org/10.1002/lno.11076  

   McParland, Erin L. ; Levine, Naomi M. ( November 2018 , Limnology and Oceanography)

   Dimethylsulfoniopropionate (DMSP) is an important labile component of the marine dissolved organic matter pool that is produced by the majority of eukaryotic marine phytoplankton and by many prokaryotes. Despite decades of research, the contribution of different environmental drivers of DMSP production to regional and seasonal variability remains unknown. A synthesis of the current state‐of‐knowledge suggested that approximately half of confirmed DMSP producers are low producers (intracellular DMSP < 50 mM). Low DMSP producers (LoDPs; e.g., diatoms) were shown to strongly regulate intracellular DMSP concentrations (~ 16‐fold change) as a predictable function of nutrient stress. By comparison, high DMSP producers (HiDPs; e.g., coccolithophores) showed very little response (~ 1.5‐fold change). To assess the importance of differential DMSP production by low and high producers, DMSP concentrations were predicted for two time‐series sites (a high‐ and low‐productivity site) and for the global ocean by explicitly incorporating both community composition and mechanistic nutrient stress. Despite large, predictable intracellular DMSP changes, low producers contributed less than 5% to global DMSP. This indicates that, while variations in DMSP production by low producers could be important for predicting microbial interactions and low producer physiology, it is not necessary for predicting global DMSP concentrations. Our analysis suggests that community composition, particularly HiDP biomass, is the dominant driver of variability in in situ DMSP concentrations, even in low‐productivity regions where high producers are typically the subdominant group. Accurate predictions of in situ DMSP concentrations require improved representation of subdominant community dynamics in ecosystem models and remote‐sensing algorithms.

    

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