ISME communications最新文献_第8页

Enrichment of different taxa of the enigmatic candidate phyla radiation bacteria using a novel picolitre droplet technique. 利用新型皮升液滴技术富集神秘候选门类辐射细菌的不同类群。

IF 5.1

ISME communications Pub Date : 2024-06-21 eCollection Date: 2024-01-01 DOI: 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":"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, Cand. Jorgensenbacteria, and unclassified UBA9983. Furthermore, we identified co-enriched putative host taxa, which may guide more targeted CPR isolation approaches in subsequent investigations.","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}

引用次数: 0

Multikingdom oral microbiome interactions in early-onset cryptogenic ischemic stroke. 早发隐源性缺血性脑卒中中多组口腔微生物群的相互作用。

IF 5.1

ISME communications Pub Date : 2024-06-20 eCollection Date: 2024-01-01 DOI: 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":"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 (n = 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.","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}

引用次数: 0

Increasing aggregate size reduces single-cell organic carbon incorporation by hydrogel-embedded wetland microbes. 增大聚合体尺寸可减少嵌入水凝胶的湿地微生物对单细胞有机碳的吸收。

IF 5.1

ISME communications Pub Date : 2024-06-20 eCollection Date: 2024-01-01 DOI: 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":"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 (Flavobacterium sp.), and in a second experiment with a microbial community from an urban lacustrine wetland. The hydrogel-embedded microbial populations were incubated with 13C-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.","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}

引用次数: 0

Driving through stop signs: predicting stop codon reassignment improves functional annotation of bacteriophages. 驶过停止标志：预测停止密码子重配可改进噬菌体的功能注释。

IF 5.1

ISME communications Pub Date : 2024-06-19 eCollection Date: 2024-01-01 DOI: 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":"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 Crassvirales, 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.","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}

引用次数: 0

Transcriptomic insights into the shift of trophic strategies in mixotrophic dinoflagellate Lepidodinium in the warming ocean. 通过转录组深入了解暖化海洋中混养甲藻营养策略的转变。

IF 5.1

ISME communications Pub Date : 2024-06-19 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae087

Jiawei Chen, Lixia Deng, Mengwen Pang, Yingdong Li, Zhimeng Xu, Xiaodong Zhang, Hongbin Liu

{"title":"Transcriptomic insights into the shift of trophic strategies in mixotrophic dinoflagellate Lepidodinium 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":"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 Lepidodinium 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 Lepidodinium sp. when cryptophyte prey were added. We further compared the expression profiles of photosynthesis and phagocytosis genes in Lepidodinium sp. in the global sunlit ocean. Our results indicated that Lepidodinium sp. became more phagotrophic with increasing temperatures when the ambient chlorophyll concentration was >0.3 mg.m-3 (~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-3 (~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.","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}

引用次数: 0

Active prokaryotic and eukaryotic viral ecology across spatial scale in a deep-sea brine pool. 深海盐池中跨空间尺度的活性原核和真核病毒生态学。

IF 5.1

ISME communications Pub Date : 2024-06-14 eCollection Date: 2024-01-01 DOI: 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":"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.","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}

引用次数: 0

Metabolically-versatile Ca. Thiodiazotropha symbionts of the deep-sea lucinid clam Lucinoma kazani have the genetic potential to fix nitrogen. 代谢易变的 Ca.深海琉璃蛤（Lucinoma kazani）的硫代滋养菌共生体具有固氮的遗传潜力。

ISME communications Pub Date : 2024-06-04 eCollection Date: 2024-01-01 DOI: 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 Lucinoma kazani 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":"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 Lucinoma kazani 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 in situ gene expression, metabolism and physiology of the symbionts. We found genes needed for N2 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.","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}

引用次数: 0

Hackflex library preparation enables low-cost metagenomic profiling. Hackflex 文库制备实现了低成本的元基因组剖析。

IF 5.1

ISME communications Pub Date : 2024-05-29 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae075

Samantha L Goldman, Jon G Sanders, Daniel D Sprockett, Abigail Landers, Weiwei Yan, Andrew H Moeller

{"title":"Hackflex library preparation enables low-cost metagenomic profiling.","authors":"Samantha L Goldman, Jon G Sanders, Daniel D Sprockett, Abigail Landers, Weiwei Yan, Andrew H Moeller","doi":"10.1093/ismeco/ycae075","DOIUrl":"10.1093/ismeco/ycae075","url":null,"abstract":"Shotgun metagenomic sequencing provides valuable insights into microbial communities, but the high cost of library preparation with standard kits and protocols is a barrier for many. New methods such as Hackflex use diluted commercially available reagents to greatly reduce library preparation costs. However, these methods have not been systematically validated for metagenomic sequencing. Here, we evaluate Hackflex performance by sequencing metagenomic libraries from known mock communities as well as mouse fecal samples prepared by Hackflex, Illumina DNA Prep, and Illumina TruSeq methods. Hackflex successfully recovered all members of the Zymo mock community, performing best for samples with DNA concentrations <1 ng/μL. Furthermore, Hackflex was able to delineate microbiota of individual inbred mice from the same breeding stock at the same mouse facility, and statistical modeling indicated that mouse ID explained a greater fraction of the variance in metagenomic composition than did library preparation method. These results show that Hackflex is suitable for generating inventories of bacterial communities through metagenomic sequencing.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae075"},"PeriodicalIF":5.1,"publicationDate":"2024-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11190725/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141443868","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}

引用次数: 0

Interactions between the nitrogen-fixing cyanobacterium Trichodesmium and siderophore-producing cyanobacterium Synechococcus under iron limitation. 铁限制条件下固氮蓝藻毛囊藻与产铁蓝藻Synechococcus之间的相互作用。

ISME communications Pub Date : 2024-05-25 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae072

Xumei Sun, Yan Xiao, Chengwen Yong, Hansheng Sun, Shuangqing Li, Hailong Huang, Haibo Jiang

{"title":"Interactions between the nitrogen-fixing cyanobacterium Trichodesmium and siderophore-producing cyanobacterium Synechococcus under iron limitation.","authors":"Xumei Sun, Yan Xiao, Chengwen Yong, Hansheng Sun, Shuangqing Li, Hailong Huang, Haibo Jiang","doi":"10.1093/ismeco/ycae072","DOIUrl":"10.1093/ismeco/ycae072","url":null,"abstract":"As diazotrophic cyanobacteria of tremendous biomass, Trichodesmium continuously provide a nitrogen source for carbon-fixing cyanobacteria and drive the generation of primary productivity in marine environments. However, ocean iron deficiencies limit growth and metabolism of Trichodesmium. Recent studies have shown the co-occurrence of Trichodesmium and siderophore-producing Synechococcus in iron-deficient oceans, but whether siderophores secreted by Synechococcus can be used by Trichodesmium to adapt to iron deficiency is not clear. We constructed a mutant Synechococcus strain unable to produce siderophores to explore this issue. Synechococcus filtrates with or without siderophores were added into a Trichodesmium microbial consortium consisting of Trichodesmium erythraeum IMS 101 as the dominant microbe with chronic iron deficiency. By analyzing the physiological phenotype, metagenome, and metatranscriptome, we investigated the interactions between the nitrogen-fixing cyanobacterium Tricodesmium and siderophore-producing cyanobacterium Synechococcus under conditions of iron deficiency. The results indicated that siderophores secreted by Synechococcus are likely to chelate with free iron in the culture medium of the Trichodesmium consortium, reducing the concentration of bioavailable iron and posing greater challenges to the absorption of iron by Trichodesmium. These findings revealed the characteristics of iron-competitive utilization between diazotrophic cyanobacteria and siderophore-producing cyanobacteria, as well as potential interactions, and provide a scientific basis for understanding the regulatory effects of nutrient limitation on marine primary productivity.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae072"},"PeriodicalIF":0.0,"publicationDate":"2024-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11171426/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141319089","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}

引用次数: 0

Mixed waste contamination selects for a mobile genetic element population enriched in multiple heavy metal resistance genes. 混合废物污染选择了富含多种重金属抗性基因的移动遗传元素种群。

ISME communications Pub Date : 2024-05-09 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae064

Jennifer L Goff, Lauren M Lui, Torben N Nielsen, Farris L Poole, Heidi J Smith, Kathleen F Walker, Terry C Hazen, Matthew W Fields, Adam P Arkin, Michael W W Adams

{"title":"Mixed waste contamination selects for a mobile genetic element population enriched in multiple heavy metal resistance genes.","authors":"Jennifer L Goff, Lauren M Lui, Torben N Nielsen, Farris L Poole, Heidi J Smith, Kathleen F Walker, Terry C Hazen, Matthew W Fields, Adam P Arkin, Michael W W Adams","doi":"10.1093/ismeco/ycae064","DOIUrl":"10.1093/ismeco/ycae064","url":null,"abstract":"Mobile genetic elements (MGEs) like plasmids, viruses, and transposable elements can provide fitness benefits to their hosts for survival in the presence of environmental stressors. Heavy metal resistance genes (HMRGs) are frequently observed on MGEs, suggesting that MGEs may be an important driver of adaptive evolution in environments contaminated with heavy metals. Here, we report the meta-mobilome of the heavy metal-contaminated regions of the Oak Ridge Reservation subsurface. This meta-mobilome was compared with one derived from samples collected from unimpacted regions of the Oak Ridge Reservation subsurface. We assembled 1615 unique circularized DNA elements that we propose to be MGEs. The circular elements from the highly contaminated subsurface were enriched in HMRG clusters relative to those from the nearby unimpacted regions. Additionally, we found that these HMRGs were associated with Gamma and Betaproteobacteria hosts in the contaminated subsurface and potentially facilitate the persistence and dominance of these taxa in this region. Finally, the HMRGs were associated with conjugative elements, suggesting their potential for future lateral transfer. We demonstrate how our understanding of MGE ecology, evolution, and function can be enhanced through the genomic context provided by completed MGE assemblies.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae064"},"PeriodicalIF":0.0,"publicationDate":"2024-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11128244/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141155249","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}

引用次数: 0