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1. The ALPINE–ALMA [C ii] Survey: The Infrared–Radio Correlation and Active Galactic Nucleus Fraction of Star-forming Galaxies at z ∼ 4.4–5.9

   https://doi.org/10.3847/1538-4357/ac81c5  

   Shen, Lu; Lemaux, Brian C.; Lubin, Lori M.; Liu, Guilin; Béthermin, Matthieu; Boquien, Médéric; Cucciati, Olga; Le Fèvre, Olivier; Talia, Margherita; Vergani, Daniela; et al (August 2022, The Astrophysical Journal)

   Abstract We present the radio properties of 66 spectroscopically confirmed normal star-forming galaxies (SFGs) at 4.4 <z< 5.9 in the COSMOS field that were [Cii]-detected in the Atacama Large Millimeter/submillimeter Array Large Program to INvestigate [Cii] at Early times (ALPINE). We separate these galaxies (“Cii-detected-all”) into lower-redshift (“Cii-detected-lz”; 〈z〉 = 4.5) and higher-redshift (“Cii-detected-hz”; 〈z〉 = 5.6) subsamples, and stack multiwavelength imaging for each subsample from X-ray to radio bands. A radio signal is detected in the stacked 3 GHz images of the Cii-detected-all and lz samples at ≳3σ. We find that the infrared–radio correlation of our sample, quantified byq_TIR, is lower than the local relation for normal SFGs at a ∼3σsignificance level, and is instead broadly consistent with that of bright submillimeter galaxies at 2 <z< 5. Neither of these samples show evidence of dominant active galactic nucleus activity in their stacked spectral energy distributions (SEDs), UV spectra, or stacked X-ray images. Although we cannot rule out the possible effects of the assumed spectral index and applied infrared SED templates in causing these differences, at least partially, the lower obscured fraction of star formation than at lower redshift can alleviate the tension between our stackedq_TIRs and those of local normal SFGs. It is possible that the dust buildup, which primarily governs the infrared emission, in addition to older stellar populations, has not had enough time to occur fully in these galaxies, whereas the radio emission can respond on a more rapid timescale. Therefore, we might expect a lowerq_TIRto be a general property of high-redshift SFGs. 

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2. Differential gene expression associated with fungal trophic shifts along the senescence gradient of the moss Dicranum scoparium

   https://doi.org/10.1111/1462-2920.14605  

   Chen, Ko‐Hsuan; Liao, Hui‐Ling; Bellenger, Jean‐Philippe; Lutzoni, François (April 2019, Environmental Microbiology)

   Summary Bryophytes harbour microbiomes, including diverse communities of fungi. The molecular mechanisms by which perennial mosses interact with these fungal partners along their senescence gradients are unknown, yet this is an ideal system to study variation in gene expression associated with trophic state transitions. We investigated differentially expressed genes of fungal communities and their hostDicranum scopariumacross its naturally occurring senescence gradient using a metatranscriptomic approach. Higher activity of fungal nutrient‐related (carbon, nitrogen, phosphorus and sulfur) transporters and Carbohydrate‐Active enZyme (CAZy) genes was detected toward the bottom, partially decomposed, layer of the moss. The most prominent variation in the expression levels of fungal nutrient transporters was from inorganic nitrogen‐related transporters, whereas the breakdown of organonitrogens was detected as the most enriched gene ontology term for the hostD. scoparium, for those transcripts having higher expression in the partially decomposed layer. The abundance of bacterial rRNA transcripts suggested that more living members ofCyanobacteriaare associated with the photosynthetic layer ofD. scoparium, while members ofRhizobialesare detected throughout the gametophytes. Plant genes for specific fungal–plant communication, including defense responses, were differentially expressed, suggesting that different genetic pathways are involved in plant‐microbe crosstalk in photosynthetic tissues compared to partially decomposed tissues. 

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3. Role of cytosolic, tyrosine‐insensitive prephenate dehydrogenase in Medicago truncatula

   https://doi.org/10.1002/pld3.218  

   Schenck, Craig A.; Westphal, Josh; Jayaraman, Dhileepkumar; Garcia, Kevin; Wen, Jiangqi; Mysore, Kirankumar S.; Ané, Jean‐Michel; Sumner, Lloyd W.; Maeda, Hiroshi A. (May 2020, Plant Direct)

   Abstract l‐Tyrosine (Tyr) is an aromatic amino acid synthesized de novo in plants and microbes downstream of the shikimate pathway. In plants, Tyr and a Tyr pathway intermediate, 4‐hydroxyphenylpyruvate (HPP), are precursors to numerous specialized metabolites, which are crucial for plant and human health. Tyr is synthesized in the plastids by a TyrA family enzyme, arogenate dehydrogenase (ADH/TyrA_a), which is feedback inhibited by Tyr. Additionally, many legumes possess prephenate dehydrogenases (PDH/TyrA_p), which are insensitive to Tyr and localized to the cytosol. Yet the role of PDH enzymes in legumes is currently unknown. This study isolated and characterizedTnt1‐transposon mutants ofMtPDH1(pdh1) inMedicago truncatulato investigate PDH function. The pdh1mutants lackedPDHtranscript and PDH activity, and displayed little aberrant morphological phenotypes under standard growth conditions, providing genetic evidence thatMtPDH1is responsible for the PDH activity detected inM. truncatula. Though plant PDH enzymes and activity have been specifically found in legumes, nodule number and nitrogenase activity ofpdh1 mutants were not significantly reduced compared with wild‐type (Wt) during symbiosis with nitrogen‐fixing bacteria. Although Tyr levels were not significantly different between Wt and mutants under standard conditions, when carbon flux was increased by shikimate precursor feeding, mutants accumulated significantly less Tyr than Wt. These data suggest that MtPDH1 is involved in Tyr biosynthesis when the shikimate pathway is stimulated and possibly linked to unidentified legume‐specific specialized metabolism. 

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4. Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer

   https://doi.org/10.1038/s41598-019-53679-0  

   Orellana, Luis H.; Hatt, Janet K.; Iyer, Ramsunder; Chourey, Karuna; Hettich, Robert L.; Spain, Jim C.; Yang, Wendy H.; Chee-Sanford, Joanne C.; Sanford, Robert A.; Löffler, Frank E.; et al (November 2019, Scientific Reports)

   Abstract To what extent multi-omic techniques could reflectin situmicrobial process rates remains unclear, especially for highly diverse habitats like soils. Here, we performed microcosm incubations using sandy soil from an agricultural site in Midwest USA. Microcosms amended with isotopically labeled ammonium and urea to simulate a fertilization event showed nitrification (up to 4.1 ± 0.87 µg N-NO₃⁻g⁻¹dry soil d⁻¹) and accumulation of N₂O after 192 hours of incubation. Nitrification activity (NH₄⁺ → NH₂OH → NO → NO₂^- → NO₃⁻) was accompanied by a 6-fold increase in relative expression of the 16S rRNA gene (RNA/DNA) between 10 and 192 hours of incubation for ammonia-oxidizing bacteriaNitrosomonasandNitrosospira, unlike archaea and comammox bacteria, which showed stable gene expression. A strong relationship between nitrification activity and betaproteobacterial ammonia monooxygenase and nitrite oxidoreductase transcript abundances revealed that mRNA quantitatively reflected measured activity and was generally more sensitive than DNA under these conditions. Although peptides related to housekeeping proteins from nitrite-oxidizing microorganisms were detected, their abundance was not significantly correlated with activity, revealing that meta-proteomics provided only a qualitative assessment of activity. Altogether, these findings underscore the strengths and limitations of multi-omic approaches for assessing diverse microbial communities in soils and provide new insights into nitrification. 

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5. Metatranscriptomic analysis reveals dissimilarity in viral community activity between an ice-free and ice-covered winter in Lake Erie

   https://doi.org/10.1128/msystems.00753-24  

   Denison, Elizabeth R; Zepernick, Brittany N; McKay, R_Michael L; Wilhelm, Steven W (July 2024, mSystems)

   Blanchard, Jeffrey Lawrence (Ed.)

   ABSTRACT Winter is a relatively under-studied season in freshwater ecology. The paucity of wintertime surveys has led to a lack of knowledge regarding microbial community activity during the winter in Lake Erie, a North American Great Lake. Viruses shape microbial communities and regulate biogeochemical cycles by acting as top-down controls, yet very few efforts have been made to examine active virus populations during the winter in Lake Erie. Furthermore, climate change-driven declines in seasonal ice cover have been shown to influence microbial community structure, but no studies have compared viral community activity between different ice cover conditions. We surveyed surface water metatranscriptomes for viral hallmark genes as a proxy for active virus populations and compared activity metrics between ice-covered and ice-free conditions from two sampled winters. Transcriptionally active viral communities were detected in both winters, spanning diverse phylogenetic clades of putative bacteriophage (Caudoviricetes), giant viruses (Nucleocytoviricota, or NCLDV), and RNA viruses (Orthornavirae). However, viral community activity metrics revealed pronounced differences between the ice-covered and ice-free winters. Viral community composition was distinct between winters and viral hallmark gene richness was reduced in the ice-covered relative to the ice-free conditions. In addition, the observed differences in viral communities correlated with microbial community activity metrics. Overall, these findings contribute to our understanding of the viral populations that are active during the winter in Lake Erie and suggest that viral community activity may be associated with ice cover extent.IMPORTANCEAs seasonal ice cover is projected to become increasingly rare on large temperate lakes, there is a need to understand how microbial communities might respond to changing ice conditions. Although it is widely recognized that viruses impact microbial community structure and function, there is little known regarding wintertime viral activity or the relationship between viral activity and ice cover extent. Our metatranscriptomic analyses indicated that viruses were transcriptionally active in the winter surface waters of Lake Erie. These findings also expanded the known diversity of viral lineages in the Great Lakes. Notably, viral community activity metrics were significantly different between the two sampled winters. The pronounced differences we observed in active viral communities between the ice-covered and ice-free samples merit further research regarding how viral communities will function in future, potentially ice-free, freshwater systems. 

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