Mosquitoes transmit a wide variety of devastating pathogens when they bite vertebrate hosts and feed on their blood. However, three entire mosquito genera and many individual species in other genera have evolved a nonbiting life history in which blood is not required to produce eggs. Our long-term goal is to develop novel interventions that reduce or eliminate the biting behavior in vector mosquitoes. A previous study used biting and nonbiting populations of a nonvector mosquito, Wyeomyia smithii, as a model to uncover the transcriptional basis of the evolutionary transition from a biting to a nonbiting life history. Herein, we ask whether the molecular pathways that were differentially expressed due to differences in biting behavior in W. smithii are also differentially expressed between subspecies of Culex pipiens that are obligate biting (Culex pipiens pipiens) and facultatively nonbiting (Culex pipiens molestus). Results from RNAseq of adult heads show dramatic upregulation of transcripts in the ribosomal protein pathway in biting C. pipiens, recapitulating the results in W. smithii, and implicating the ancient and highly conserved ribosome as the intersection to understanding the evolutionary and physiological basis of blood feeding in mosquitoes. Biting Culex also strongly upregulate energy production pathways, including oxidative phosphorylation and the citric acid (TCA) cycle relative to nonbiters, a distinction that was not observed in W. smithii. Amino acid metabolism pathways were enriched for differentially expressed genes in biting versus nonbiting Culex. Relative to biters, nonbiting Culex upregulated sugar metabolism and transcripts contributing to reproductive allocation (vitellogenin and cathepsins). These results provide a foundation for developing strategies to determine the natural evolutionary transition between a biting and nonbiting life history in vector mosquitoes.
more »
« less
Transcriptional activity differentiates families of Marine Group II Euryarchaeota in the coastal ocean
Abstract Marine Group II Euryarchaeota ( Candidatus Poseidoniales), abundant but yet-uncultivated members of marine microbial communities, are thought to be (photo)heterotrophs that metabolize dissolved organic matter (DOM), such as lipids and peptides. However, little is known about their transcriptional activity. We mapped reads from a metatranscriptomic time series collected at Sapelo Island (GA, USA) to metagenome-assembled genomes to determine the diversity of transcriptionally active Ca . Poseidoniales. Summer metatranscriptomes had the highest abundance of Ca . Poseidoniales transcripts, mostly from the O1 and O3 genera within Ca . Thalassarchaeaceae (MGIIb). In contrast, transcripts from fall and winter samples were predominantly from Ca . Poseidoniaceae (MGIIa). Genes encoding proteorhodopsin, membrane-bound pyrophosphatase, peptidase/proteases, and part of the ß-oxidation pathway were highly transcribed across abundant genera. Highly transcribed genes specific to Ca . Thalassarchaeaceae included xanthine/uracil permease and receptors for amino acid transporters. Enrichment of Ca . Thalassarchaeaceae transcript reads related to protein/peptide, nucleic acid, and amino acid transport and metabolism, as well as transcript depletion during dark incubations, provided further evidence of heterotrophic metabolism. Quantitative PCR analysis of South Atlantic Bight samples indicated consistently abundant Ca . Poseidoniales in nearshore and inshore waters. Together, our data suggest that Ca . Thalassarchaeaceae are important photoheterotrophs potentially linking DOM and nitrogen cycling in coastal waters.
more »
« less
- PAR ID:
- 10226057
- Date Published:
- Journal Name:
- ISME Communications
- Volume:
- 1
- Issue:
- 1
- ISSN:
- 2730-6151
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Abstract Genes in SARS-CoV-2 and other viruses in the order ofNidoviralesare expressed by a process of discontinuous transcription which is distinct from alternative splicing in eukaryotes and is mediated by the viral RNA-dependent RNA polymerase. Here, we introduce the DISCONTINUOUS TRANSCRIPT ASSEMBLYproblem of finding transcripts and their abundances given an alignment of paired-end short reads under a maximum likelihood model that accounts for varying transcript lengths. We show, using simulations, that our method, JUMPER, outperforms existing methods for classical transcript assembly. On short-read data of SARS-CoV-1, SARS-CoV-2 and MERS-CoV samples, we find that JUMPER not only identifies canonical transcripts that are part of the reference transcriptome, but also predicts expression of non-canonical transcripts that are supported by subsequent orthogonal analyses. Moreover, application of JUMPER on samples with and without treatment reveals viral drug response at the transcript level. As such, JUMPER enables detailed analyses ofNidoviralestranscriptomes under varying conditions.more » « less
-
Most methods for statistical analysis of RNA-seq data take a matrix of abundance estimates for some type of genomic features as their input, and consequently the quality of any obtained results is directly dependent on the quality of these abundances. Here, we present the junction coverage compatibility score, which provides a way to evaluate the reliability of transcript-level abundance estimates and the accuracy of transcript annotation catalogs. It works by comparing the observed number of reads spanning each annotated splice junction in a genomic region to the predicted number of junction-spanning reads, inferred from the estimated transcript abundances and the genomic coordinates of the corresponding annotated transcripts. We show that although most genes show good agreement between the observed and predicted junction coverages, there is a small set of genes that do not. Genes with poor agreement are found regardless of the method used to estimate transcript abundances, and the corresponding transcript abundances should be treated with care in any downstream analyses.more » « less
-
null (Ed.)Carbonyl sulfide (COS) and carbon disulfide (CS 2 ) are important atmospheric gases that are formed from organic sulfur precursors present in natural waters when exposed to sunlight. However, it remains unclear how specific water constituents, such as dissolved organic matter (DOM), affect COS and CS 2 formation. To better understand the role of DOM, irradiation experiments were conducted in O 2 -free synthetic waters containing four different DOM isolates, acquired from freshwater to open ocean sources, and the sulfur-based amino acid, cysteine (CYS). CYS is a known natural precursor of COS and CS 2 . Results indicated that COS formation did not vary strongly with DOM type, although small impacts were observed on the kinetic patterns. COS formation also increased with increasing CYS concentration but decreased with increasing DOM concentration. Quenching experiments indicated that ˙OH was not involved in the rate-limiting step of COS formation, whereas excited triplet states of DOM ( 3 CDOM*) were plausibly involved, although the quenching agents used to remove 3 CDOM* may have reacted with the CYS-derived intermediates as well. CS 2 was not formed under any of the experimental conditions. Overall, DOM-containing synthetic waters had a limited to no effect towards forming COS and CS 2 , especially when compared to the higher concentrations formed in sunlit natural waters, as examined previously. The reasons behind this limited effect need to be explored further but may be due to the additional water quality constituents present in these natural waters. The findings of this study imply that multiple variables beyond DOM govern COS and CS 2 photoproduction when moving from freshwaters to open ocean waters.more » « less
-
Biddle, Jennifer F (Ed.)ABSTRACT The abundant and metabolically versatile aquatic bacterial order,Rhodobacterales, influences marine biogeochemical cycles. We assessedRhodobacteralesmetagenome-assembled genome (MAG) abundance, estimated growth rates, and potential and expressed functions in the Chesapeake and Delaware Bays, two important US estuaries. Phylogenomics of draft and draft/closedRhodobacteralesgenomes from this study and others placed 46 nearly complete MAGs from these bays into 11 genera, many were not well characterized. Their abundances varied between the bays and were influenced by temperature, salinity, and silicate and phosphate concentrations.Rhodobacteralesgenera possessed unique and shared genes for transporters, photoheterotrophy, complex carbon degradation, nitrogen, and sulfur metabolism reflecting their seasonal differences in abundance and activity.Planktomarinagenomospecies were more ubiquitous than the more niche specialists, HIMB11, CPC320, LFER01, and MED-G52. Their estimated growth rates were correlated to various factors including phosphate and silicate concentrations, cell density, and light. Metatranscriptomic analysis of four abundant genomospecies commonly revealed that aerobic anoxygenic photoheterotrophy-associated transcripts were highly abundant at night. TheseRhodobacteralesalso differentially expressed genes for CO oxidation and nutrient transport and use between different environmental conditions. Phosphate concentrations and light penetration in the Chesapeake Bay likely contributed to higher estimated growth rates of HIMB11 and LFER01, respectively, in summer where they maintained higher ribosome concentrations and prevented physiological gene expression constraints by downregulating transporter genes compared to the Delaware Bay. Our study highlights the spatial and temporal shifts in estuarineRhodobacteraleswithin and between these bays reflected through their abundance, unique metabolisms, estimated growth rates, and activity changes. IMPORTANCEIn the complex web of global biogeochemical nutrient cycling, theRhodobacteralesemerge as key players, exerting a profound influence through their abundance and dynamic activity. While previous studies have primarily investigated these organisms within marine ecosystems, this study delves into their roles within estuarine environments using a combination of metagenomic and metatranscriptomic analyses. We uncovered a range ofRhodobacteralesgenera, from generalists to specialists, each exhibiting distinct abundance patterns and gene expression profiles. This diversity equips them with the capacity to thrive amidst the varying environmental conditions encountered within dynamic estuarine habitats. Crucially, our findings illuminate the adaptable nature of estuarineRhodobacterales, revealing their various energy production pathways and diverse resource management, especially during phytoplankton or algal blooms. Whether adopting a free-living or particle-attached existence, these organisms demonstrate remarkable flexibility in their metabolic strategies, underscoring their pivotal role in driving ecosystem dynamics within estuarine ecosystems.more » « less
An official website of the United States government

