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At least 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Assessing biogeographic survey gaps in bacterial diversity knowledge: A global synthesis of freshwaters

Freshwaters account for 0.8% of Earth's surface area, yet support >10% of known plant and animal species making them disproportionately biodiverse. Modern molecular techniques have begun to reveal microbial diversity, but application of these approaches to address global microbial biogeography is relatively unknown in freshwaters. Our aim was to identify gaps in microbial data coverage along climatic and landscape disturbance gradients and among terrestrial biomes and hydrographic regions for all freshwater ecosystems and three freshwater habitat types: lakes and reservoirs (lentic); streams and rivers (lotic); and wetlands. We reviewed literature on microbial diversity in freshwaters surveyed using 16S ribosomal RNA sequencing which identify microbial taxa. We georeferenced survey locations and used a geographic information system to identify and map gaps in survey coverage using open-source data for climate, landscape disturbance, terrestrial biomes, and freshwater ecoregions. In our study, we compiled 3,425 georeferenced survey locations reported from 963 studies. Streams were surveyed most frequently (60.8% of survey locations), followed by lakes (33.5%) and wetlands (5.6%). Surveys were concentrated in North America, central and western Europe, and Southeast Asia; 35% of freshwater ecoregions were surveyed at least once across freshwater habitat types, whereas 23%, 23%, and 12% were surveyed at least once for lentic, lotic, and wetland habitat types, respectively. The climatic gap analysis indicated coverage is high for temperate regions but lacking in the tropics and Arctic, particularly for wetland ecosystems. Our assessment revealed high climatic coverage of freshwater microbial diversity knowledge, but expansive ecoregional gaps attributable to biased sampling near research institutions in North America, western Europe, and China. Future surveys should target ecoregions in Africa, South America, Central Asia, Australia, and Antarctica. An essential next step will be to curate and disseminate sequencing efforts to facilitate the study of processes driving global diversity patterns.

16S rRNA↗
DOE OSTI2024

PagMYB128 regulates secondary cell wall formation by direct activation of cell wall biosynthetic genes during wood formation in poplar

The biosynthesis of cellulose, lignin, and hemicelluloses in plant secondary cell walls (SCWs) is regulated by a hierarchical transcriptional regulatory network. Here, this network features orthologous transcription factors shared between poplar and Arabidopsis, highlighting a foundational similarity in their genetic regulation. However, knowledge on the discrepant behavior of the transcriptional-level molecular regulatory mechanisms between poplar and Arabidopsis remains limited. In this study, we investigated the function of PagMYB128 during wood formation and found it had broader impacts on SCW formation compared to its Arabidopsis ortholog, AtMYB103. Transgenic poplar trees overexpressing PagMYB128 exhibited significantly enhanced xylem development, with fiber cells and vessels displaying thicker walls, and an increase in the levels of cellulose, lignin, and hemicelluloses in the wood. In contrast, plants with dominant repression of PagMYB128 demonstrated the opposite phenotypes. RNA sequencing and reverse transcription – quantitative polymerase chain reaction showed that PagMYB128 could activate SCW biosynthetic gene expression, and chromatin immunoprecipitation along with yeast one-hybrid, and effector–reporter assays showed this regulation was direct. Further analysis revealed that PagSND1 (SECONDARY WALL-ASSOCIATED NAC-DOMAIN PROTEIN1) directly regulates PagMYB128 but not cell wall metabolic genes, highlighting the pivotal role of PagMYB128 in the SND1-driven regulatory network for wood development, thereby creating a feedforward loop in SCW biosynthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Abscisic acid supports colonization of Eucalyptus grandis roots by the mutualistic ectomycorrhizal fungus Pisolithus microcarpus

Summary The pathways regulated in ectomycorrhizal (EcM) plant hosts during the establishment of symbiosis are not as well understood when compared to the functional stages of this mutualistic interaction. Our study used the EcM host Eucalyptus grandis to elucidate symbiosis‐regulated pathways across the three phases of this interaction. Using a combination of RNA sequencing and metabolomics we studied both stage‐specific and core responses of E. grandis during colonization by Pisolithus microcarpus . Using exogenous manipulation of the abscisic acid (ABA), we studied the role of this pathway during symbiosis establishment. Despite the mutualistic nature of this symbiosis, a large number of disease signalling TIR‐NBS‐LRR genes were induced. The transcriptional regulation in E. grandis was found to be dynamic across colonization with a small core of genes consistently regulated at all stages. Genes associated to the carotenoid/ABA pathway were found within this core and ABA concentrations increased during fungal integration into the root. Supplementation of ABA led to improved accommodation of P. microcarpus into E. grandis roots. The carotenoid pathway is a core response of an EcM host to its symbiont and highlights the need to understand the role of the stress hormone ABA in controlling host–EcM fungal interactions.

Hill, Richard A.↗
DOE OSTI2022

Identification of new marker genes from plant single‐cell RNA‐seq data using interpretable machine learning methods

Summary An essential step in the analysis of single‐cell RNA sequencing data is to classify cells into specific cell types using marker genes. In this study, we have developed a machine learning pipeline called single‐cell predictive marker (SPmarker) to identify novel cell‐type marker genes in the Arabidopsis root. Unlike traditional approaches, our method uses interpretable machine learning models to select marker genes. We have demonstrated that our method can: assign cell types based on cells that were labelled using published methods; project cell types identified by trajectory analysis from one data set to other data sets; and assign cell types based on internal GFP markers. Using SPmarker, we have identified hundreds of new marker genes that were not identified before. As compared to known marker genes, the new marker genes have more orthologous genes identifiable in the corresponding rice single‐cell clusters. The new root hair marker genes also include 172 genes with orthologs expressed in root hair cells in five non‐ Arabidopsis species, which expands the number of marker genes for this cell type by 35–154%. Our results represent a new approach to identifying cell‐type marker genes from scRNA‐seq data and pave the way for cross‐species mapping of scRNA‐seq data in plants.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Osmotic stress-responsive promoter upstream transcripts (PROMPTs) act as carriers of MYB transcription factors to induce the expression of target genes in Populus simonii

Complex RNA transcription and processing produces a diverse range catalog of long noncoding RNAs (lncRNAs), important biological regulators that have been implicated in osmotic stress responses in plants. Promoter upstream transcript (PROMPT) lncRNAs share some regulatory elements with the promoters of their neighbouring protein-coding genes. However, their function remains unknown. Here, using strand-specific RNA sequencing, we identified 209 differentially regulated osmotic-responsive PROMPTs in poplar (Populus simonii). PROMPTs are transcribed bidirectionally and are more stable than other lncRNAs. Co-expression analysis of PROMPTs and protein-coding genes divided the regulatory network into five independent subnetworks including 27 network modules. Significantly enriched PROMPTs in the network were selected to validate their regulatory roles. We used delaminated layered double hydroxide lactate nanosheets (LDH-lactate-NS) to transport synthetic nucleic acids into live tissues to mimic overexpression and interference of a specific PROMPT. The altered expression of PROMPT_1281 induced the expression of its cis and trans targets, and this interaction was governed by its secondary structure rather than just its primary sequence. Based on this example, we proposed a model that a concentration gradient of PROMPT_1281 is established, which increases the probability of its interaction with targets near its transcription site that shares common motifs. Our results firstly demonstrated that PROMPT_1281 act as carriers of MYB transcription factors to induce the expression of target genes under osmotic stress. In sum, our study identified and validated a set of poplar PROMPTs that likely have regulatory functions in osmotic responses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Complex interactions between day length and diurnal patterns of gene expression drive photoperiodic responses in a perennial C 4 grass

Abstract Photoperiod is a key environmental cue affecting flowering and biomass traits in plants. Key components of the photoperiodic flowering pathway have been identified in many species, but surprisingly few studies have globally examined the diurnal rhythm of gene expression with changes in day length. Using a cost‐effective 3′‐Tag RNA sequencing strategy, we characterize 9,010 photoperiod responsive genes with strict statistical testing across a diurnal time series in the C 4 perennial grass, Panicum hallii . We show that the vast majority of photoperiod responses are driven by complex interactions between day length and sampling periods. A fine‐scale contrast analysis at each sampling time revealed a detailed picture of the temporal reprogramming of cis ‐regulatory elements and biological processes under short‐ and long‐day conditions. Phase shift analysis reveals quantitative variation among genes with photoperiod‐dependent diurnal patterns. In addition, we identify three photoperiod enriched transcription factor families with key genes involved in photoperiod flowering regulatory networks. Finally, coexpression networks analysis of GIGANTEA homolog predicted 1,668 potential coincidence partners, including five well‐known GI‐interacting proteins. Our results not only provide a resource for understanding the mechanisms of photoperiod regulation in perennial grasses but also lay a foundation to increase biomass yield in biofuel crops.

Weng, Xiaoyu↗
DOE OSTI2019

An ectomycorrhizal fungus alters sensitivity to jasmonate, salicylate, gibberellin, and ethylene in host roots

The phytohormones jasmonate, gibberellin, salicylate, and ethylene regulate an interconnected reprogramming network integrating root development with plant responses against microbes. The establishment of mutualistic ectomycorrhizal symbiosis requires the suppression of plant defense responses against fungi as well as the modification of root architecture and cortical cell wall properties. In this work, we investigated the contribution of phytohormones and their crosstalk to the ontogenesis of ectomycorrhizae (ECM) between grey poplar (Populus tremula x alba) roots and the fungus Laccaria bicolor. To obtain the hormonal blueprint of developing ECM, we quantified the concentrations of jasmonates, gibberellins, and salicylate via liquid chromatography-tandem mass spectrometry. Subsequently, we assessed root architecture, mycorrhizal morphology, and gene expression levels (RNA sequencing) in phytohormone-treated poplar lateral roots in the presence or absence of L. bicolor. Salicylic acid accumulated in mid-stage ECM. Exogenous phytohormone treatment affected the fungal colonization rate and/or frequency of Hartig net formation. Colonized lateral roots displayed diminished responsiveness to jasmonate but regulated some genes, implicated in defense and cell wall remodelling, that were specifically differentially expressed after jasmonate treatment. Responses to salicylate, gibberellin, and ethylene were enhanced in ECM. The dynamics of phytohormone accumulation and response suggest that jasmonate, gibberellin, salicylate, and ethylene signalling play multifaceted roles in poplar L. bicolor ectomycorrhizal development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Enzymatic basis for C‐lignin monomer biosynthesis in the seed coat of Cleome hassleriana

Summary C‐lignin is a linear polymer of caffeyl alcohol, found in the seed coats of several exotic plant species, with promising properties for generation of carbon fibers and high value chemicals. In the ornamental plant Cleome hassleriana , guaiacyl (G) lignin is deposited in the seed coat for the first 6–12 days after pollination, after which G‐lignin deposition ceases and C‐lignin accumulates, providing an excellent model system to study C‐lignin biosynthesis. We performed RNA sequencing of seed coats harvested at 2‐day intervals throughout development. Bioinformatic analysis identified a complete set of lignin biosynthesis genes for Cleome . Transcript analysis coupled with kinetic analysis of recombinant enzymes in Escherichia coli revealed that the switch to C‐lignin formation was accompanied by down‐regulation of transcripts encoding functional caffeoyl CoA‐ and caffeic acid 3‐ O ‐methyltransferases ( CC o AOMT and COMT ) and a form of cinnamyl alcohol dehydrogenase (Ch CAD 4) with preference for coniferaldehyde as substrate, and up‐regulation of a form of CAD (Ch CAD 5) with preference for caffealdehyde. Based on these analyses, blockage of lignin monomer methylation by down‐regulation of both O ‐methyltransferases ( OMT s) and methionine synthase (for provision of C1 units) appears to be the major factor in diversion of flux to C‐lignin in the Cleome seed coat, although the change in CAD specificity also contributes based on the reduction of C‐lignin levels in transgenic Cleome with down‐regulation of Ch CAD 5. Structure modeling and mutational analysis identified amino acid residues important for the preference of Ch CAD 5 for caffealdehyde.

Zhuo, Chunliu↗
DOE OSTI2024

Multilevel analysis between Physcomitrium patens and Mortierellaceae endophytes explores potential long‐standing interaction among land plants and fungi

SUMMARY The model moss species Physcomitrium patens has long been used for studying divergence of land plants spanning from bryophytes to angiosperms. In addition to its phylogenetic relationships, the limited number of differential tissues, and comparable morphology to the earliest embryophytes provide a system to represent basic plant architecture. Based on plant–fungal interactions today, it is hypothesized these kingdoms have a long‐standing relationship, predating plant terrestrialization. Mortierellaceae have origins diverging from other land fungi paralleling bryophyte divergence, are related to arbuscular mycorrhizal fungi but are free‐living, observed to interact with plants, and can be found in moss microbiomes globally. Due to their parallel origins, we assess here how two Mortierellaceae species, Linnemannia elongata and Benniella erionia , interact with P. patens in coculture. We also assess how Mollicute ‐related or Burkholderia ‐related endobacterial symbionts (MRE or BRE) of these fungi impact plant response. Coculture interactions are investigated through high‐throughput phenomics, microscopy, RNA‐sequencing, differential expression profiling, gene ontology enrichment, and comparisons among 99 other P. patens transcriptomic studies. Here we present new high‐throughput approaches for measuring P. patens growth, identify novel expression of over 800 genes that are not expressed on traditional agar media, identify subtle interactions between P. patens and Mortierellaceae, and observe changes to plant–fungal interactions dependent on whether MRE or BRE are present. Our study provides insights into how plants and fungal partners may have interacted based on their communications observed today as well as identifying L. elongata and B. erionia as modern fungal endophytes with P. patens .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

NF-κB perturbation reveals unique immunomodulatory functions in Prx1 + fibroblasts that promote development of atopic dermatitis

Skin is composed of diverse cell populations that cooperatively maintain homeostasis. Up-regulation of the nuclear factor κB (NF-κB) pathway may lead to the development of chronic inflammatory disorders of the skin, but its role during the early events remains unclear. Here, through analysis of single-cell RNA sequencing data via iterative random forest leave one out prediction, an explainable artificial intelligence method, we identified an immunoregulatory role for a unique paired related homeobox-1 (Prx1) + fibroblast subpopulation. Disruption of Ikkb–NF-κB under homeostatic conditions in these fibroblasts paradoxically induced skin inflammation due to the overexpression of C-C motif chemokine ligand 11 (CCL11; or eotaxin-1) characterized by eosinophil infiltration and a subsequent T H 2 immune response. Because the inflammatory phenotype resembled that seen in human atopic dermatitis (AD), we examined human AD skin samples and found that human AD fibroblasts also overexpressed CCL11 and that perturbation of Ikkb–NF-κB in primary human dermal fibroblasts up-regulated CCL11. Monoclonal antibody treatment against CCL11 was effective in reducing the eosinophilia and T H 2 inflammation in a mouse model. Together, the murine model and human AD specimens point to dysregulated Prx1 + fibroblasts as a previously unrecognized etiologic factor that may contribute to the pathogenesis of AD and suggest that targeting CCL11 may be a way to treat AD-like skin lesions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Nitrate-Utilizing Microorganisms Resistant to Multiple Metals from the Heavily Contaminated Oak Ridge Reservation.

Contamination of environments with nitrate generated by industrial processes and the use of nitrogen-containing fertilizers is a growing problem worldwide. While nitrate can be removed from contaminated areas by microbial denitrification, nitrate frequently occurs with other contaminants, such as heavy metals, that have the potential to impede the process. In this work, nitrate-reducing microorganisms were enriched and isolated from both groundwater and sediments at the Oak Ridge Reservation (ORR) using concentrations of nitrate and metals (Al, Mn, Fe, Co, Ni, Cu, Cd, and U) similar to those observed in a contaminated environment at ORR. Seven new metal-resistant, nitrate-reducing strains were characterized, and their distribution across both noncontaminated and contaminated areas at ORR was examined. Additionally, while the seven strains have various pH ranges for growth, carbon source preferences, and degrees of resistance to individual and combinations of metals, all were able to reduce nitrate at similar rates both in the presence and absence of the mixture of metals found in the contaminated ORR environment. Four strains were identified in groundwater samples at different ORR locations by exact 16S RNA sequence variant analysis, and all four were found in both noncontaminated and contaminated areas. By using environmentally relevant metal concentrations, we successfully isolated multiple organisms from both ORR noncontaminated and contaminated environments that are capable of reducing nitrate in the presence of extreme mixed-metal contamination.IMPORTANCE Nitrate contamination is a global issue that affects groundwater quality. In some cases, cocontamination of groundwater with nitrate and mixtures of heavy metals could decrease microbially mediated nitrate removal, thereby increasing the duration of nitrate contamination. In this study, we used metal and nitrate concentrations that are present in a contaminated site at the Oak Ridge Reservation to isolate seven metal-resistant strains. All were able to reduce nitrate in the presence of high concentrations of a mixture of heavy metals. Four of seven strains were located in pristine as well as contaminated sites at the Oak Ridge Reservation. Further study of these nitrate-reducing strains will uncover mechanisms of resistance to multiple metals that will increase our understanding of the effect of nitrate and metal contamination on groundwater microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Conservation of Transcription Start Sites within Genes across a Bacterial Genus

Transcription start sites (TSSs) lying inside annotated genes, on the same or opposite strand, have been observed in diverse bacteria, but the function of these unexpected transcripts is unclear. Here, we use the metal-reducing bacterium Shewanella oneidensis MR-1 and its relatives to study the evolutionary conservation of unexpected TSSs. Using high-resolution tiling microarrays and 5'-end RNA sequencing, we identified 2,531 TSSs in S. oneidensis MR-1, of which 18% were located inside coding sequences (CDSs). Comparative transcriptome analysis with seven additional Shewanella species revealed that the majority (76%) of the TSSs within the upstream regions of annotated genes (gTSSs) were conserved. Thirty percent of the TSSs that were inside genes and on the sense strand (iTSSs) were also conserved. Sequence analysis around these iTSSs showed conserved promoter motifs, suggesting that many iTSS are under purifying selection. Furthermore, conserved iTSSs are enriched for regulatory motifs, suggesting that they are regulated, and they tend to eliminate polar effects, which confirms that they are functional. In contrast, the transcription of antisense TSSs located inside CDSs (aTSSs) was significantly less likely to be conserved (22%). However, aTSSs whose transcription was conserved often have conserved promoter motifs and drive the expression of nearby genes. Overall, our findings demonstrate that some internal TSSs are conserved and drive protein expression despite their unusual locations, but the majority are not conserved and may reflect noisy initiation of transcription rather than a biological function.

bacterial genus↗
DOE OSTI2024

Spatiotemporal analysis of lung immune dynamics in lethal Coccidioides posadasii infection

Coccidioidomycosis, or Valley fever, is a lung disease caused by inhalation of Coccidioides fungi, prevalent in the Southwestern United States, Mexico, and parts of Central and South America. Annually, the United States reports 10,000–20,000 cases, although those numbers are expected to increase as climate change expands the fungal geographic range. While 60% of infections are asymptomatic, 40% symptomatic infections are often misdiagnosed due to similarities with bronchitis or pneumonia. A small subset of infection progress to severe illness, necessitating a better understanding of immune responses during lethal infection. Using single-cell RNA sequencing and spatial transcriptomics, we characterized lung responses during Coccidioides infection. We identified monocyte-derived Spp1-expressing macrophages as potential mediators of tissue remodeling and fibrosis, marked by high expression of profibrotic and proinflammatory transcripts. These macrophages showed elevated TGF-β and IL-6 signaling, pathways involved in fibrosis pathogenesis. Additionally, we observed significant neutrophil infiltration and defective lymphocyte responses, indicating severe adaptive immunity dysregulation in lethal, acute infection. These findings enhance our understanding of Coccidioides infection and suggest new therapeutic targets.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Transcriptomic and functional analyses uncover a conserved effector driving genotype-dependent virulence in the Sphaerulina musiva-Populus trichocarpa interaction

The introduction of invasive microbes compromises the structure, biodiversity, and function of naïve ecosystems. Sphaerulina musiva, a hemibiotrophic pathogen that causes leaf spot and stem cankers in Populus species, exemplifies an invasive fungal pathogen spread by human activities. However, the genetic mechanisms of pathogenicity and virulence are poorly understood, impeding mitigation strategies. We utilized RNA sequencing to identify fungal effectors linked to stem canker formation, informing the development of future strategies for effective disease management. Our analysis revealed 70 genes differentially expressed at 2 weeks and 110 genes at 3 weeks between inoculated trees and controls. Notably, the gene with the highest expression at 2 weeks and the second highest at 3 weeks was homologous to Extracellular protein 2 (Ecp2). Complementary genome-wide association studies linked sequence polymorphisms in this locus to phenotypic variation in disease severity. Infiltration of S. musiva Ecp2 into Populus trichocarpa leaves induced necrosis in susceptible genotypes. Gene disruption using a CRISPR-Cas9 RNP system resulted in a genotype-dependent reduction of stem canker and disease severity. Tracing the evolutionary history of this effector across the fungal kingdom, we uncovered clade-specific gene-family expansions and orthologs in new species. These findings raise questions about the function and adaptive significance of these gene families in fungal lifestyles. Our study provides the first tractable target for breeding resistant poplar genotypes, addressing the challenges of managing S. musiva and uncovering mechanisms that drive its virulence, and provides deeper insights into the evolutionary dynamics of a conserved small-secreted protein with a diversity of functions.

Sondreli, Kelsey L [Oregon State University]↗
DOE OSTI2025

Transcriptomic data sets for Novosphingobium aromaticivorans DSM12444 and a ΔSARO_RS14285 mutant grown in the presence of glucose and either protocatechuic, vanillic, syringic, or 4-coumaric acid

The SARO_RS14285 gene, encoding a transcription factor, was deleted in Novosphingobium aromaticivorans DSM12444. The transcriptomes of the parent and ΔSARO_RS14285 strains were determined when grown in medium containing glucose with or without protocatechuic, vanillic, syringic, or 4-coumaric acid. We present the raw RNA sequencing data obtained from these cultures.

Novosphingobium aromaticivorans↗
DOE OSTI2024

Transcriptomic data sets for Novosphingobium aromaticivorans grown with the β-5-linked aromatic dimer dehydrodiconiferyl alcohol and the related G-aromatic monomers vanillin and ferulic acid

ABSTRACT The transcriptomes of a 2-pyrone-4,6-dicarboxylic acid-producing strain of Novosphingobium aromaticivorans DSM12444 were determined when grown in minimal medium containing glucose alone or glucose plus vanillin, ferulic acid, or the β-5-linked aromatic dimer dehydrodiconiferyl alcohol as carbon sources. Here, we present the RNA-sequencing data we obtained.

Metz, Fletcher↗
DOE OSTI2025

Separate, separated, and together: the transcriptional program of the Clostridium acetobutylicum-Clostridium ljungdahlii syntrophy leading to interspecies cell fusion

ABSTRACT Syntrophic cocultures (hitherto assumed to be commensalistic) of Clostridium acetobutylicum and Clostridium ljungdahlii , whereby CO 2 and H 2 produced by the former feed the latter, result in interspecies cell fusion involving large-scale exchange of protein, RNA, and DNA between the two organisms. Although mammalian cell fusion is mechanistically dissected, the mechanism for such microbial-cell fusions is unknown. To start exploring this mechanism, we used RNA sequencing to identify genes differentially expressed in this coculture using two types of comparisons. One type compared coculture to the two monocultures, capturing the combined impact of interactions through soluble signals in the medium and through direct cell-to-cell interactions. The second type compared membrane-separated versus -unseparated cocultures, isolating the impact of interspecies physical contact. While we could not firmly identify specific genes that might drive cell fusion, consistent with our hypothesized model for this interspecies microbial cell fusion, we observed differential regulation of genes involved in C. ljungdahlii’s autotrophic Wood-Ljungdahl pathway metabolism and genes of the motility machinery. Unexpectedly, we also identified differential regulation of biosynthetic genes of several amino acids, and notably of arginine and histidine. We verified that they are produced by C. acetobutylicum and are metabolized by C. ljungdahlii to its growth advantage. These and other findings, and notably upregulation of C. acetobutylicum ribosomal-protein genes, paint a more complex syntrophic picture and suggest a mutualistic relationship, whereby beyond CO 2 and H 2 , C. acetobutylicum feeds C. ljungdahlii with growth-boosting amino acids, while benefiting from the H 2 utilization by C. ljungdahlii . IMPORTANCE The construction and study of synthetic microbial cocultures is a growing research area due to the untapped potential of defined multi-species industrial bioprocesses and the utility of defined cocultures for generating insight into complex, undefined, natural microbial consortia. Our previous work showed that coculturing C. acetobutylicum and C. ljungdahlii leads to a unique metabolic phenotype (production of isopropanol) and heterologous cell fusion events. Here, we used RNAseq to explore genes involved in and impacted by these fusions. First, we compared gene expression in coculture to each monoculture. Second, we utilized a transwell system to compare gene expression in mixed cocultures to cocultures with both species physically separated by a permeable membrane, isolating the impact of interspecies “touching” on the transcriptome. This study deepens our mechanistic understanding of the C. acetobutylicum-C. ljungdahlii coculture phenotype, laying the groundwork for reverse genetic studies of heterologous cell fusion in Clostridium cocultures.

Willis, Noah B. (ORCID:0009000689365955)↗