ISME communicationsPub Date : 2024-07-15eCollection Date: 2024-01-01DOI: 10.1093/ismeco/ycae098
Linda Armbrecht, Christopher J S Bolch, Bradley Paine, Alan Cooper, Andrew McMinn, Craig Woodward, Gustaaf Hallegraeff
{"title":"Recovering sedimentary ancient DNA of harmful dinoflagellates accumulated over the last 9000 years off Eastern Tasmania, Australia.","authors":"Linda Armbrecht, Christopher J S Bolch, Bradley Paine, Alan Cooper, Andrew McMinn, Craig Woodward, Gustaaf Hallegraeff","doi":"10.1093/ismeco/ycae098","DOIUrl":"10.1093/ismeco/ycae098","url":null,"abstract":"<p><p>Harmful algal blooms (HABs) have had significant adverse impacts on the seafood industry along the Tasmanian east coast over the past 4 decades. To investigate the history of regional HABs, we performed analyses of sedimentary ancient DNA (<i>sed</i>aDNA) in coastal sediments up to ~9000 years old collected inshore and offshore of Maria Island, Tasmania. We used metagenomic shotgun sequencing and a hybridisation capture array (\"HABbaits1\") to target three harmful dinoflagellate genera, <i>Alexandrium</i>, <i>Gymnodinium</i>, and <i>Noctiluca</i>. Bioinformatic and DNA damage analyses verified the authenticity of the <i>sed</i>aDNA sequences. Our results show that dinoflagellates of <i>Alexandrium</i> genera have been present off eastern Tasmania during the last ~8300 years, and we sporadically detected and unambiguously verified sequences of <i>Gymnodinium catenatum</i> that were present offshore up to ~7600 years ago. We also recovered <i>sed</i>aDNA of the fragile, soft-bodied <i>Noctiluca scintillans</i> with increased relative abundance since 2010, consistent with plankton surveys. This study enabled us to identify challenges of <i>sed</i>aDNA sequence validation (in particular for <i>G. catenatum</i>, a microreticulate gymnodinoid species) and provided guidance for the development of tools to monitor past and present HAB species and improvement of future HAB event predictions.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae098"},"PeriodicalIF":5.1,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11334580/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142010049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ISME communicationsPub Date : 2024-07-12eCollection Date: 2024-01-01DOI: 10.1093/ismeco/ycae085
Robert M Bowers, Veronica Gonzalez-Pena, Kartika Wardhani, Danielle Goudeau, Matthew James Blow, Daniel Udwary, David Klein, Albert C Vill, Ilana L Brito, Tanja Woyke, Rex R Malmstrom, Charles Gawad
{"title":"scMicrobe PTA: near complete genomes from single bacterial cells.","authors":"Robert M Bowers, Veronica Gonzalez-Pena, Kartika Wardhani, Danielle Goudeau, Matthew James Blow, Daniel Udwary, David Klein, Albert C Vill, Ilana L Brito, Tanja Woyke, Rex R Malmstrom, Charles Gawad","doi":"10.1093/ismeco/ycae085","DOIUrl":"10.1093/ismeco/ycae085","url":null,"abstract":"<p><p>Microbial genomes produced by standard single-cell amplification methods are largely incomplete. Here, we show that primary template-directed amplification (PTA), a novel single-cell amplification technique, generated nearly complete genomes from three bacterial isolate species. Furthermore, taxonomically diverse genomes recovered from aquatic and soil microbiomes using PTA had a median completeness of 81%, whereas genomes from standard multiple displacement amplification-based approaches were usually <30% complete. PTA-derived genomes also included more associated viruses and biosynthetic gene clusters.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae085"},"PeriodicalIF":5.1,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11253033/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141636020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ISME communicationsPub Date : 2024-06-21eCollection Date: 2024-01-01DOI: 10.1093/ismeco/ycae089
Dimitri Meier, Sigrid van Grinsven, Anja Michel, Philip Eickenbusch, Clemens Glombitza, Xingguo Han, Annika Fiskal, Stefano Bernasconi, Carsten J Schubert, Mark A Lever
{"title":"Hydrogen-independent CO<sub>2</sub> reduction dominates methanogenesis in five temperate lakes that differ in trophic states.","authors":"Dimitri Meier, Sigrid van Grinsven, Anja Michel, Philip Eickenbusch, Clemens Glombitza, Xingguo Han, Annika Fiskal, Stefano Bernasconi, Carsten J Schubert, Mark A Lever","doi":"10.1093/ismeco/ycae089","DOIUrl":"10.1093/ismeco/ycae089","url":null,"abstract":"<p><p>Emissions of microbially produced methane (CH<sub>4</sub>) from lake sediments are a major source of this potent greenhouse gas to the atmosphere. The rates of CH<sub>4</sub> production and emission are believed to be influenced by electron acceptor distributions and organic carbon contents, which in turn are affected by anthropogenic inputs of nutrients leading to eutrophication. Here, we investigate how eutrophication influences the abundance and community structure of CH<sub>4</sub> producing <i>Archaea</i> and methanogenesis pathways across time-resolved sedimentary records of five Swiss lakes with well-characterized trophic histories. Despite higher CH<sub>4</sub> concentrations which suggest higher methanogenic activity in sediments of eutrophic lakes, abundances of methanogens were highest in oligotrophic lake sediments. Moreover, while the methanogenic community composition differed significantly at the lowest taxonomic levels (OTU), depending on whether sediment layers had been deposited under oligotrophic or eutrophic conditions, it showed no clear trend in relation to <i>in situ</i> distributions of electron acceptors. Remarkably, even though methanogenesis from CO<sub>2</sub>-reduction was the dominant pathway in all sediments based on carbon isotope fractionation values, taxonomic identities, and genomes of resident methanogens, CO<sub>2</sub>-reduction with hydrogen (H<sub>2</sub>) was thermodynamically unfavorable based on measured reactant and product concentrations. Instead, strong correlations between genomic abundances of CO<sub>2</sub>-reducing methanogens and anaerobic bacteria with potential for extracellular electron transfer suggest that methanogenic CO<sub>2</sub>-reduction in lake sediments is largely powered by direct electron transfer from syntrophic bacteria without involvement of H<sub>2</sub> as an electron shuttle.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae089"},"PeriodicalIF":5.1,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11235125/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141581737","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ISME communicationsPub Date : 2024-06-21eCollection Date: 2024-01-01DOI: 10.1093/ismeco/ycae080
DeDe Kwun Wai Man, Syrie M Hermans, Martin Taubert, Sarahi L Garcia, Sundar Hengoju, Kirsten Küsel, Miriam A Rosenbaum
{"title":"Enrichment of different taxa of the enigmatic candidate phyla radiation bacteria using a novel picolitre droplet technique.","authors":"DeDe Kwun Wai Man, Syrie M Hermans, Martin Taubert, Sarahi L Garcia, Sundar Hengoju, Kirsten Küsel, Miriam A Rosenbaum","doi":"10.1093/ismeco/ycae080","DOIUrl":"10.1093/ismeco/ycae080","url":null,"abstract":"<p><p>The candidate phyla radiation (CPR) represents a distinct monophyletic clade and constitutes a major portion of the tree of life. Extensive efforts have focused on deciphering the functional diversity of its members, primarily using sequencing-based techniques. However, cultivation success remains scarce, presenting a significant challenge, particularly in CPR-dominated groundwater microbiomes characterized by low biomass. Here, we employ an advanced high-throughput droplet microfluidics technique to enrich CPR taxa from groundwater. Utilizing a low-volume filtration approach, we successfully harvested a microbiome resembling the original groundwater microbial community. We assessed CPR enrichment in droplet and aqueous bulk cultivation for 30 days using a novel CPR-specific primer to rapidly track the CPR fraction through the cultivation attempts. The combination of soil extract and microbial-derived necromass provided the most supportive conditions for CPR enrichment. Employing these supplemented conditions, droplet cultivation proved superior to bulk cultivation, resulting in up to a 13-fold CPR enrichment compared to a 1- to 2-fold increase in bulk cultivation. Amplicon sequencing revealed 10 significantly enriched CPR orders. The highest enrichment in CPRs was observed for some unknown members of the Parcubacteria order, <i>Cand</i>. Jorgensenbacteria, and unclassified UBA9983. Furthermore, we identified co-enriched putative host taxa, which may guide more targeted CPR isolation approaches in subsequent investigations.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae080"},"PeriodicalIF":5.1,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11214157/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141473263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ISME communicationsPub Date : 2024-06-20eCollection Date: 2024-01-01DOI: 10.1093/ismeco/ycae088
Muhammed Manzoor, Jaakko Leskelä, Milla Pietiäinen, Nicolas Martinez-Majander, Pauli Ylikotila, Eija Könönen, Teemu Niiranen, Leo Lahti, Juha Sinisalo, Jukka Putaala, Pirkko J Pussinen, Susanna Paju
{"title":"Multikingdom oral microbiome interactions in early-onset cryptogenic ischemic stroke.","authors":"Muhammed Manzoor, Jaakko Leskelä, Milla Pietiäinen, Nicolas Martinez-Majander, Pauli Ylikotila, Eija Könönen, Teemu Niiranen, Leo Lahti, Juha Sinisalo, Jukka Putaala, Pirkko J Pussinen, Susanna Paju","doi":"10.1093/ismeco/ycae088","DOIUrl":"10.1093/ismeco/ycae088","url":null,"abstract":"<p><p>Although knowledge of the role of the oral microbiome in ischemic stroke is steadily increasing, little is known about the multikingdom microbiota interactions and their consequences. We enrolled participants from a prospective multicentre case-control study and investigated multikingdom microbiome differences using saliva metagenomic datasets (<i>n</i> = 308) from young patients diagnosed with cryptogenic ischemic stroke (CIS) and age- and sex-matched stroke-free controls. Differentially abundant taxa were identified using Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC2). Functional potential was inferred using HUMANn3. Our findings revealed significant differences in the composition and functional capacity of the oral microbiota associated with CIS. We identified 51 microbial species, including 47 bacterial, 3 viral, and one fungal species associated with CIS in the adjusted model. Co-abundance network analysis highlighted a more intricate microbial network in CIS patients, indicating potential interactions and co-occurrence patterns among microbial species across kingdoms. The results of our metagenomic analysis reflect the complexity of the oral microbiome, with high diversity and multikingdom interactions, which may play a role in health and disease.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae088"},"PeriodicalIF":5.1,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11235082/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141581738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ISME communicationsPub Date : 2024-06-20eCollection Date: 2024-01-01DOI: 10.1093/ismeco/ycae086
Juliet T Johnston, Bao Nguyen Quoc, Britt Abrahamson, Pieter Candry, Christina Ramon, Kevin J Cash, Sam C Saccomano, Ty J Samo, Congwang Ye, Peter K Weber, Mari-Karoliina Henriikka Winkler, Xavier Mayali
{"title":"Increasing aggregate size reduces single-cell organic carbon incorporation by hydrogel-embedded wetland microbes.","authors":"Juliet T Johnston, Bao Nguyen Quoc, Britt Abrahamson, Pieter Candry, Christina Ramon, Kevin J Cash, Sam C Saccomano, Ty J Samo, Congwang Ye, Peter K Weber, Mari-Karoliina Henriikka Winkler, Xavier Mayali","doi":"10.1093/ismeco/ycae086","DOIUrl":"10.1093/ismeco/ycae086","url":null,"abstract":"<p><p>Microbial degradation of organic carbon in sediments is impacted by the availability of oxygen and substrates for growth. To better understand how particle size and redox zonation impact microbial organic carbon incorporation, techniques that maintain spatial information are necessary to quantify elemental cycling at the microscale. In this study, we produced hydrogel microspheres of various diameters (100, 250, and 500 μm) and inoculated them with an aerobic heterotrophic bacterium isolated from a freshwater wetland (<i>Flavobacterium</i> sp.)<i>,</i> and in a second experiment with a microbial community from an urban lacustrine wetland. The hydrogel-embedded microbial populations were incubated with <sup>13</sup>C-labeled substrates to quantify organic carbon incorporation into biomass via nanoSIMS. Additionally, luminescent nanosensors enabled spatially explicit measurements of oxygen concentrations inside the microspheres. The experimental data were then incorporated into a reactive-transport model to project long-term steady-state conditions. Smaller (100 μm) particles exhibited the highest microbial cell-specific growth per volume, but also showed higher absolute activity near the surface compared to the larger particles (250 and 500 μm). The experimental results and computational models demonstrate that organic carbon availability was not high enough to allow steep oxygen gradients and as a result, all particle sizes remained well-oxygenated. Our study provides a foundational framework for future studies investigating spatially dependent microbial activity in aggregates using isotopically labeled substrates to quantify growth.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae086"},"PeriodicalIF":5.1,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11227278/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141556059","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ISME communicationsPub Date : 2024-06-19eCollection Date: 2024-01-01DOI: 10.1093/ismeco/ycae079
Ryan Cook, Andrea Telatin, George Bouras, Antonio Pedro Camargo, Martin Larralde, Robert A Edwards, Evelien M Adriaenssens
{"title":"Driving through stop signs: predicting stop codon reassignment improves functional annotation of bacteriophages.","authors":"Ryan Cook, Andrea Telatin, George Bouras, Antonio Pedro Camargo, Martin Larralde, Robert A Edwards, Evelien M Adriaenssens","doi":"10.1093/ismeco/ycae079","DOIUrl":"10.1093/ismeco/ycae079","url":null,"abstract":"<p><p>The majority of bacteriophage diversity remains uncharacterized, and new intriguing mechanisms of their biology are being continually described. Members of some phage lineages, such as the <i>Crassvirales</i>, repurpose stop codons to encode an amino acid by using alternate genetic codes. Here, we investigated the prevalence of stop codon reassignment in phage genomes and its subsequent impacts on functional annotation. We predicted 76 genomes within INPHARED and 712 vOTUs from the Unified Human Gut Virome Catalogue (UHGV) that repurpose a stop codon to encode an amino acid. We re-annotated these sequences with modified versions of Pharokka and Prokka, called Pharokka-gv and Prokka-gv, to automatically predict stop codon reassignment prior to annotation. Both tools significantly improved the quality of annotations, with Pharokka-gv performing best. For sequences predicted to repurpose TAG to glutamine (translation table 15), Pharokka-gv increased the median gene length (median of per genome median) from 287 to 481 bp for UHGV sequences (67.8% increase) and from 318 to 550 bp for INPHARED sequences (72.9% increase). The re-annotation increased median coding capacity from 66.8% to 90.0% and from 69.0% to 89.8% for UHGV and INPHARED sequences predicted to use translation table 15. Furthermore, the proportion of genes that could be assigned functional annotation increased, including an increase in the number of major capsid proteins that could be identified. We propose that automatic prediction of stop codon reassignment before annotation is beneficial to downstream viral genomic and metagenomic analyses.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae079"},"PeriodicalIF":5.1,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11210395/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141473262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Transcriptomic insights into the shift of trophic strategies in mixotrophic dinoflagellate <i>Lepidodinium</i> in the warming ocean.","authors":"Jiawei Chen, Lixia Deng, Mengwen Pang, Yingdong Li, Zhimeng Xu, Xiaodong Zhang, Hongbin Liu","doi":"10.1093/ismeco/ycae087","DOIUrl":"10.1093/ismeco/ycae087","url":null,"abstract":"<p><p>The shift between photoautotrophic and phagotrophic strategies in mixoplankton significantly impacts the planktonic food webs and biogeochemical cycling. Considering the projected global warming, studying how temperature impacts this shift is crucial. Here, we combined the transcriptome of in-lab cultures (mixotrophic dinoflagellate <i>Lepidodinium</i> sp.) and the metatranscriptome dataset of the global ocean to investigate the mechanisms underlying the shift of trophic strategies and its relationship with increasing temperatures. Our results showed that phagocytosis-related pathways, including focal adhesion, regulation of actin cytoskeleton, and oxidative phosphorylation, were significantly stimulated in <i>Lepidodinium</i> sp. when cryptophyte prey were added. We further compared the expression profiles of photosynthesis and phagocytosis genes in <i>Lepidodinium</i> sp. in the global sunlit ocean. Our results indicated that <i>Lepidodinium</i> sp. became more phagotrophic with increasing temperatures when the ambient chlorophyll concentration was >0.3 mg.m<sup>-3</sup> (~20.58% of the ocean surface) but became more photoautotrophic with increasing temperatures when the chlorophyll concentration was between 0.2 and 0.3 mg.m<sup>-3</sup> (~11.47% of the ocean surface). Overall, we emphasized the crucial role of phagocytosis in phago-mixotrophy and suggested that the expression profile of phagocytosis genes can be a molecular marker to target the phagotrophic activity of mixoplankton in situ.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae087"},"PeriodicalIF":5.1,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11247192/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141621858","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ISME communicationsPub Date : 2024-06-14eCollection Date: 2024-01-01DOI: 10.1093/ismeco/ycae084
Benjamin Minch, Morgan Chakraborty, Sam Purkis, Mattie Rodrigue, Mohammad Moniruzzaman
{"title":"Active prokaryotic and eukaryotic viral ecology across spatial scale in a deep-sea brine pool.","authors":"Benjamin Minch, Morgan Chakraborty, Sam Purkis, Mattie Rodrigue, Mohammad Moniruzzaman","doi":"10.1093/ismeco/ycae084","DOIUrl":"10.1093/ismeco/ycae084","url":null,"abstract":"<p><p>Deep-sea brine pools represent rare, extreme environments, providing unique insight into the limits of life on Earth, and by analogy, the plausibility of life beyond it. A distinguishing feature of many brine pools is presence of thick microbial mats that develop at the brine-seawater interface. While these bacterial and archaeal communities have received moderate attention, viruses and their host interactions in these environments remain underexplored. To bridge this knowledge gap, we leveraged metagenomic and metatranscriptomic data from three distinct zones within the NEOM brine pool system (Gulf of Aqaba) to reveal the active viral ecology around the pools. We report a remarkable diversity and activity of viruses infecting microbial hosts in this environment, including giant viruses, RNA viruses, jumbo phages, and Polinton-like viruses. Many of these form distinct clades-suggesting presence of untapped viral diversity in this ecosystem. Brine pool viral communities exhibit zone-specific differences in infection strategy-with lysogeny dominating the bacterial mat further away from the pool's center. We linked viruses to metabolically important prokaryotes-including association between a jumbo phage and a key manganese-oxidizing and arsenic-metabolizing bacterium. These foundational results illuminate the role of viruses in modulating brine pool microbial communities and biogeochemistry through revealing novel viral diversity, host associations, and spatial heterogeneity in viral dynamics.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae084"},"PeriodicalIF":5.1,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11252502/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141636019","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ISME communicationsPub Date : 2024-06-04eCollection Date: 2024-01-01DOI: 10.1093/ismeco/ycae076
Lina Ratinskaia, Stas Malavin, Tal Zvi-Kedem, Simina Vintila, Manuel Kleiner, Maxim Rubin-Blum
{"title":"Metabolically-versatile Ca. Thiodiazotropha symbionts of the deep-sea lucinid clam <i>Lucinoma kazani</i> have the genetic potential to fix nitrogen.","authors":"Lina Ratinskaia, Stas Malavin, Tal Zvi-Kedem, Simina Vintila, Manuel Kleiner, Maxim Rubin-Blum","doi":"10.1093/ismeco/ycae076","DOIUrl":"10.1093/ismeco/ycae076","url":null,"abstract":"<p><p>Lucinid clams are one of the most diverse and widespread symbiont-bearing animal groups in both shallow and deep-sea chemosynthetic habitats. Lucinids harbor Ca. Thiodiazotropha symbionts that can oxidize inorganic and organic substrates such as hydrogen sulfide and formate to gain energy. The interplay between these key metabolic functions, nutrient uptake and biotic interactions in Ca. Thiodiazotropha is not fully understood. We collected <i>Lucinoma kazani</i> individuals from next to a deep-sea brine pool in the eastern Mediterranean Sea, at a depth of 1150 m and used Oxford Nanopore and Illumina sequencing to obtain high-quality genomes of their Ca. Thiodiazotropha gloverae symbiont. The genomes served as the basis for transcriptomic and proteomic analyses to characterize the <i>in situ</i> gene expression, metabolism and physiology of the symbionts. We found genes needed for N<sub>2</sub> fixation in the deep-sea symbiont's genome, which, to date, were only found in shallow-water Ca. Thiodiazotropha. However, we did not detect the expression of these genes and thus the potential role of nitrogen fixation in this symbiosis remains to be determined. We also found the high expression of carbon fixation and sulfur oxidation genes, which indicate chemolithoautotrophy as the key physiology of Ca. Thiodiazotropha. However, we also detected the expression of pathways for using methanol and formate as energy sources. Our findings highlight the key traits these microbes maintain to support the nutrition of their hosts and interact with them.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae076"},"PeriodicalIF":0.0,"publicationDate":"2024-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11171427/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141319090","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}