ISME communications最新文献_第5页

Inferring replication states of bacteria and viruses in enrichment cultures via long-read sequencing. 通过长读测序推断富集培养物中细菌和病毒的复制状态。

IF 5.1

ISME communications Pub Date : 2025-03-05 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf041

Sophie A Simon, André R Soares, Till L V Bornemann, Adrian Lange, Lea Griesdorn, Adrián Fuentes, Marie Dieckmann, Beate A Krok, S Emil Ruff, Michael Hügler, Cristina Moraru, Alexander J Probst

{"title":"Inferring replication states of bacteria and viruses in enrichment cultures via long-read sequencing.","authors":"Sophie A Simon, André R Soares, Till L V Bornemann, Adrian Lange, Lea Griesdorn, Adrián Fuentes, Marie Dieckmann, Beate A Krok, S Emil Ruff, Michael Hügler, Cristina Moraru, Alexander J Probst","doi":"10.1093/ismeco/ycaf041","DOIUrl":"10.1093/ismeco/ycaf041","url":null,"abstract":"Most microorganisms cannot be cultured in isolation, necessitating sophisticated methods for studying their (eco)physiology. While numerous approaches can probe the activity of given microbes in enrichment cultures, no single technique can render simultaneous data on both metabolic capacities and mobile genetic elements. Here, we apply long-read sequencing to monitor the incorporation of non-canonical bases in genome-resolved metagenomic datasets and elucidate the replication patterns of both bacteria and phages. This technology enables the simultaneous reconstruction of both prokaryotic and viral genomes (alongside genomics downstream analyses like metabolic predictions), in addition to providing information regarding their replication in enrichment cultures. By spiking the base analog 5-bromo-2'-deoxyuridine (BrdU) into activated sludge microcosms, we determined that 114 of the 118 high-quality genomes recovered were actively replicating in enrichment cultures from activated sludge and identified both slow (low BrdU incorporation and change in abundance) and rapidly replicating organisms (high BrdU incorporation and change in abundance). Some of the genomes detected exhibited regions rich in BrdU that were predicted to represent prophages in their lytic cycle. Ultimately, this novel means of monitoring the replication responses of microbes, and deciphering their genomes and active mobile genetic elements will advance and empower strategies aimed at isolating previously uncultivated microbes in pure culture.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf041"},"PeriodicalIF":5.1,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11964896/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143782235","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

A hunting ground for predatory bacteria at the Zhenbei seamount in the South China Sea. 南海镇北海底山捕食性细菌的狩猎场。

IF 5.1

ISME communications Pub Date : 2025-03-05 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf042

Zhimeng Li, Dayu Zou, Rulong Liu, Juntong Pan, Junkai Huang, Jun Ma, Liting Huang, Jiani He, Lulu Fu, Xiaowei Zheng, Minxiao Wang, Jiasong Fang, Hailiang Dong, Meng Li, Li Huang, Xin Dai

{"title":"A hunting ground for predatory bacteria at the Zhenbei seamount in the South China Sea.","authors":"Zhimeng Li, Dayu Zou, Rulong Liu, Juntong Pan, Junkai Huang, Jun Ma, Liting Huang, Jiani He, Lulu Fu, Xiaowei Zheng, Minxiao Wang, Jiasong Fang, Hailiang Dong, Meng Li, Li Huang, Xin Dai","doi":"10.1093/ismeco/ycaf042","DOIUrl":"10.1093/ismeco/ycaf042","url":null,"abstract":"Seamounts are critical marine biodiversity hot spots, while the metabolic activity of their microbial community remains largely unknown. In this study, we investigated the diversity and activity of free-living and particle-attached microorganisms in the surface, middle, and bottom layers of seawater at the Zhenbei seamount in the South China Sea using omics approaches, including 16S ribosomal RNA (rRNA)/16S rDNA ratio analysis. Over 20 phyla were detected, with Proteobacteria, Actinobacteriota, Cyanobacteria, Bacteroidota, Thaumarchaeota, and Planctomycetota being predominant. Surprisingly, Bdellovibrionota and Myxococcota, the two well-known predatory bacteria, exhibited exceptionally higher rRNA/rDNA ratios than the other phyla, with rRNA abundances being 10- or even 200-fold higher than their rDNA abundances. These metabolically active predatory bacteria are mainly uncultured species. A total of 23 Myxococcota metagenome-assembled genomes (MAGs) and 12 Bdellovibrionota MAGs were assembled. The most highly overexpressed genes frequently detected in these MAGs were those that encode flagellum and pilus proteins as well as T4-like virus tail tube protein, indicating that these predator bacteria were likely active in hunting. Our results suggest that seamounts may serve as hunting grounds for predatory bacteria, which may be involved in controlling the flows of elements and energy in the seamount microbial communities and, thus, in shaping the seamount ecosystems.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf042"},"PeriodicalIF":5.1,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11937823/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143722932","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

Warming stimulates cellulose decomposition by recruiting phylogenetically diverse but functionally similar microorganisms. 变暖通过招募系统发育不同但功能相似的微生物来刺激纤维素分解。

IF 5.1

ISME communications Pub Date : 2025-03-03 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycae152

Yifan Su, Xue Guo, Yamei Gao, Jiajie Feng, Linwei Wu, Jiesi Lei, Suo Liu, Qun Gao, Yufei Zeng, Wei Qin, Zheng Shi, Zhengxiong Liang, Zhencheng Ye, Mengting Yuan, Daliang Ning, Liyou Wu, Jizhong Zhou, Yunfeng Yang

{"title":"Warming stimulates cellulose decomposition by recruiting phylogenetically diverse but functionally similar microorganisms.","authors":"Yifan Su, Xue Guo, Yamei Gao, Jiajie Feng, Linwei Wu, Jiesi Lei, Suo Liu, Qun Gao, Yufei Zeng, Wei Qin, Zheng Shi, Zhengxiong Liang, Zhencheng Ye, Mengting Yuan, Daliang Ning, Liyou Wu, Jizhong Zhou, Yunfeng Yang","doi":"10.1093/ismeco/ycae152","DOIUrl":"10.1093/ismeco/ycae152","url":null,"abstract":"Cellulose is the most abundant component of plant litter, which is critical for terrestrial carbon cycling. Nonetheless, it remains unknown how global warming affects cellulose-decomposing microorganisms. Here, we carried out a 3-year litterbag experiment to examine cellulose decomposition undergoing +3°C warming in a tallgrass prairie. Most cellulose-associated bacteria and fungi in litterbags were also detected in bulk soil, and bacteria in litterbags had higher community-level rrn copy numbers, larger genome sizes, and higher genome guanine-cytosine (GC) contents than those in bulk soil, implying higher growth rates. Warming stimulated soil respiration by 32.3% and accelerated mass loss of cellulose, concurring with the increase in relative abundances of most functional genes associated with carbon decomposition in litterbags. Incorporating cellulose-decomposing genes into an ecosystem model reduced model parameter uncertainty and showed that warming stimulated microbial biomass, activity, and soil carbon decomposition. Collectively, our study supports a trait-centric view since cellulose-decomposing genes or genomic traits are amenable for ecosystem modeling. By characterizing the phylogenetically diverse yet functionally similar cellulose-associated microorganisms and their responses to warming, we take a step toward more precise predictions of soil carbon dynamics under future climate scenarios.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycae152"},"PeriodicalIF":5.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11892950/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143598421","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

Redox determines greenhouse gas production kinetics and metabolic traits in water-saturated thawing permafrost peat. 氧化还原决定了水饱和融化永久冻土泥炭的温室气体产生动力学和代谢特性。

IF 5.1

ISME communications Pub Date : 2025-03-03 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf009

Eira Catharine Lødrup Carlsen, Jing Wei, Franck Lejzerowicz, Sigrid Trier Kjær, Sebastian Westermann, Dag O Hessen, Peter Dörsch, Alexander Eiler

{"title":"Redox determines greenhouse gas production kinetics and metabolic traits in water-saturated thawing permafrost peat.","authors":"Eira Catharine Lødrup Carlsen, Jing Wei, Franck Lejzerowicz, Sigrid Trier Kjær, Sebastian Westermann, Dag O Hessen, Peter Dörsch, Alexander Eiler","doi":"10.1093/ismeco/ycaf009","DOIUrl":"10.1093/ismeco/ycaf009","url":null,"abstract":"Redox conditions, influenced by the availability of oxygen, are expected to dictate the rate of CO2 and CH4 production and to shape the composition and metabolism of microbial communities. Here, we use thawing permafrost peat in thermokarst water under a gradient of initial O2 concentrations to experimentally cover the variability in redox conditions potentially found across thawing landscapes. The three main greenhouse gases, CO2, CH4 and N2O, responded differently to O2 absence. CO2 production along the O2 gradient could be modeled by the Michaelis Menten equation revealing a sharp decrease when oxygen dropped under 100 μM. Under anoxic conditions CO2 yield decreased by 98% and maximum net production rate by 85% when compared to oxic conditions during the 11 days after thaw. N2O production was observed under anoxic conditions, while CH4 yield and CH4 accumulation rates did not differ across the redox gradient. The latter is due to the release of stored CH4 due to thawing. Differences between oxic and anoxic conditions were reflected in the microbial genomic composition, with changes in taxonomic and functional groups, such as N2O reducers, fermenters, denitrifiers and sulfur reducers increasing under anoxic conditions. Genomic changes towards less efficient central metabolism further explained the CO2 production yields and rates limited by O2 availability as predicted by thermodynamics. Together with the Michaelis Menten models the metabolic reconstruction pinpoint to critical thresholds of CO2 release at suboxic conditions and thus need to be considered when explaining and modeling highly variable CO2 emissions across thawing landscapes.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf009"},"PeriodicalIF":5.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11922181/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143665532","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

Estimates of microbial community stability using relative invader growth rates are robust across levels of invader species richness. 利用相对入侵者生长速率估算的微生物群落稳定性在不同的入侵物种丰富度水平上都是可靠的。

IF 5.1

ISME communications Pub Date : 2025-03-02 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf040

Meaghan Castledine, Daniel Padfield, Angus Buckling

{"title":"Estimates of microbial community stability using relative invader growth rates are robust across levels of invader species richness.","authors":"Meaghan Castledine, Daniel Padfield, Angus Buckling","doi":"10.1093/ismeco/ycaf040","DOIUrl":"https://doi.org/10.1093/ismeco/ycaf040","url":null,"abstract":"A key feature of natural communities is that the species within them stably coexist. A common metric used to test community stability is the ability of each species to invade from rare. A potential issue with this measurement is that single species are invaded from rare, while in natural communities, multiple species would likely decline simultaneously following perturbations. This is especially common in microbes which can be rapidly disturbed by environmental stressors. If species coexistence is dependent on indirect interactions among community members, multiple species declining may result in community instability. As such, invading a single species into a community may overestimate the stability of a community when multiple species decline. Here, we compare estimates of community stability in a five species microbial community to experimental results in which multiple species are simultaneously invaded. Our results showed that single species invasions were qualitatively predictive of whole community stability when multiple species are invaded simultaneously. However, quantitative values of relative invader growth rate were less comparable, being non-significantly different in most comparisons in three out of five species. This was emphasized by the lack of correlation between exact values of growth rates under single or multi-species invasion. This work provides experimental support for the robustness of using invasion growth rate of single species to infer qualitative estimates of community stability.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf040"},"PeriodicalIF":5.1,"publicationDate":"2025-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11994029/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143993397","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

Horizontal transmission of symbiotic bacteria and host selective sweep in the giant clam Tridacna crocea. 巨蛤中共生细菌的水平传播及寄主选择性清扫。

IF 5.1

ISME communications Pub Date : 2025-03-02 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf037

Cong Liu, Jian Zhang, Qiqi Li, Yuehuan Zhang, Si Zhang, Ziniu Yu, Jun Li, Jie Li

{"title":"Horizontal transmission of symbiotic bacteria and host selective sweep in the giant clam Tridacna crocea.","authors":"Cong Liu, Jian Zhang, Qiqi Li, Yuehuan Zhang, Si Zhang, Ziniu Yu, Jun Li, Jie Li","doi":"10.1093/ismeco/ycaf037","DOIUrl":"10.1093/ismeco/ycaf037","url":null,"abstract":"Giant clams, with their significant ecological importance, depend on associated bacteria for their health and development, yet the transmission modes and succession of community dynamics of these bacteria remain poorly understood. This study employed 16S rRNA gene sequencing and microscopy to investigate the transmission and community dynamics of symbiotic bacteria in the giant clam Tridacna crocea during early developmental stages (fertilized eggs, blastocyst, D-larvae, and pediveliger larvae). Fluorescence in situ hybridization and transmission electron microscopy did not detect internal symbiotic bacteria in fertilized eggs and adult gonad gametes, but scanning electron microscopy revealed microbial structures on egg surface microvilli, suggesting their role as microbial carriers. 16S rRNA sequencing confirmed microbial presence in fertilized eggs, indicating bacterial acquisition via external vertical transmission (adherence to microvilli) or horizontal transmission. Given the lack of internalized bacteria in reproductive organs, we prefer to classify the symbiotic bacteria acquisition as horizontal transmission. Microbial community analysis showed that T. crocea acquired a significant portion of its microbiome from seawater throughout its development. Before reaching the pediveliger stage, the bacterial community composition closely resembled that of the surrounding seawater, primarily featuring the family Rhodobacteraceae. As T. crocea matured, the host's selective pressure increased (e.g. deterministic assembly), which simplified the microbial community and reduced diversity. During the pediveliger stage, the genus Endozoicomonas became dominant, forming a large proportion of the bacterial community within the gonads. This highlights the ecological significance of host-microbe interactions in maintaining biodiversity and driving ecosystem stability through dynamic community assembly processes.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf037"},"PeriodicalIF":5.1,"publicationDate":"2025-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11919647/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143665530","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

Probiotics prevent mortality of thermal-sensitive corals exposed to short-term heat stress. 益生菌可以防止对热敏感的珊瑚在短期热应激下死亡。

IF 5.1

ISME communications Pub Date : 2025-03-02 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf039

Mareike de Breuyn, Malte Ostendarp, Yusuf C El-Khaled, Neus Garcias-Bonet, Susana Carvalho, Christian Wild, Raquel S Peixoto

{"title":"Probiotics prevent mortality of thermal-sensitive corals exposed to short-term heat stress.","authors":"Mareike de Breuyn, Malte Ostendarp, Yusuf C El-Khaled, Neus Garcias-Bonet, Susana Carvalho, Christian Wild, Raquel S Peixoto","doi":"10.1093/ismeco/ycaf039","DOIUrl":"10.1093/ismeco/ycaf039","url":null,"abstract":"The use of coral probiotics, i.e. beneficial microorganisms for corals (BMCs), is a novel approach to enhancing coral health under heat stress. While BMCs mitigate coral bleaching and mortality during prolonged heat stress conditions, their effectiveness in mitigating short-term acute heat stress remains understudied. This study investigates the effects of BMCs on two Red Sea hard coral species, Acropora cf. hemprichii and Pocillopora verrucosa, during short-term heat stress. Twelve coral fragments per species were allocated to each treatment across two temperature regimes (26°C and 32°C) for 48 hours, with half receiving BMC inoculation and half serving as controls. Results show BMC supplementation significantly prevented mortality in Acropora cf. hemprichii at 32°C, contrasting with a 100% mortality observed in the control group. Specifically, probiotic-inoculated Acropora cf. hemprichii at 32°C exhibited preserved primary production, a 12-13 fold increase in algal cell densities, 4-5 times higher FV/Fm ratios, and 4-5 and 2-3 times higher chlorophyll a and c2 concentrations, respectively, compared to their untreated conspecifics. All P. verrucosa colonies survived the 32°C exposure without tissue loss or reduced holobiont function in both control and BMC treatments. These findings underscore the rapid effects of BMC inoculation, initiated just 2 hours prior to acute heat stress, in protecting heat-sensitive Acropora cf. hemprichii against mortality and adverse photo-physiological changes, with beneficial effects visible within 2 days. Recognizing the critical timeframe for beneficial effects is paramount for management strategies to address heat-sensitive corals on natural reefs, such as implementing probiotic interventions before anticipated marine heatwaves.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf039"},"PeriodicalIF":5.1,"publicationDate":"2025-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11948994/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143733504","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

NifH gene amplicon sequencing and metagenomic approaches are complementary in assessing diazotroph diversity. NifH 基因扩增片段测序和元基因组学方法在评估重氮营养体多样性方面具有互补性。

IF 5.1

ISME communications Pub Date : 2025-02-27 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf038

Shunyan Cheung, Michael Morando, Jonathan Magasin, Francisco M Cornejo-Castillo, Jonathan P Zehr, Kendra A Turk-Kubo

{"title":"NifH gene amplicon sequencing and metagenomic approaches are complementary in assessing diazotroph diversity.","authors":"Shunyan Cheung, Michael Morando, Jonathan Magasin, Francisco M Cornejo-Castillo, Jonathan P Zehr, Kendra A Turk-Kubo","doi":"10.1093/ismeco/ycaf038","DOIUrl":"10.1093/ismeco/ycaf038","url":null,"abstract":"Exploring the diversity of diazotrophs is key to understanding their role in supplying fixed nitrogen that supports marine productivity. A nested PCR assay using the universal primer set nifH1-nifH4, which targets the nitrogenase (nifH) gene, is a widely used approach for studying marine diazotrophs by amplicon sequencing. Metagenomics, direct sequencing of DNA without PCR, has provided complementary views of the diversity of marine diazotrophs. A significant fraction of the metagenome-derived nifH sequences (e.g. Planctomycete- and Proteobacteria-affiliated) were reported to have nucleotide mismatches with the nifH1-nifH4 primers, leading to the suggestion that nifH amplicon sequencing does not detect specific diazotrophic taxa and underrepresents diazotroph diversity. Here, we report that these mismatches are mostly located in a single-base at the 5'-end of the nifH4 primer, which does not impact detection of the nifH genes. This is demonstrated by the presence of nifH genes that contain the nucleotide mismatches in a recent compilation of global ocean nifH amplicon datasets, with high relative abundances detected in a variety of samples. While the metagenome- and metatranscriptome-derived nifH genes accounted for 4.4% of the total amplicon sequence variants from the global ocean nifH amplicon database, the corresponding amplicon sequence variants can have high relative abundances (accounting for 47% of the reads in the database). These analyses underscore that nifH amplicon sequencing using the nifH1-nifH4 primers is an important tool for studying diversity of marine diazotrophs, particularly as a complement to metagenomics which can provide taxonomic and metabolic information for some dominant groups.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf038"},"PeriodicalIF":5.1,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11964895/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143782195","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

Identifying the active microbes driving organosulfur cycling from taurine and methionine in marine sediment. 鉴定海洋沉积物中驱动牛磺酸和蛋氨酸有机硫循环的活性微生物。

IF 5.1

ISME communications Pub Date : 2025-02-25 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf033

Ömer K Coskun, William D Orsi, Steven D'Hondt, Gonzalo V Gomez-Saez

{"title":"Identifying the active microbes driving organosulfur cycling from taurine and methionine in marine sediment.","authors":"Ömer K Coskun, William D Orsi, Steven D'Hondt, Gonzalo V Gomez-Saez","doi":"10.1093/ismeco/ycaf033","DOIUrl":"10.1093/ismeco/ycaf033","url":null,"abstract":"Studies on microbial sulfur cycling in marine sediment have primarily centered on the cycling of inorganic sulfur. The microbial diversity underlying the cycling of organosulfur compounds is largely unexplored. In this study, we present the first quantification of dissolved organic sulfur (DOS) microbial assimilation in marine surface sediments using 13C-DOS quantitative DNA stable isotope probing (qSIP). We sampled marine sediment from 493 m water depth on the Puerto Rico continental slope, measured 13C-assimilation from two DOS substrates (13C-taurine and 13C-methionine), and compared the 13C-DOS assimilation to 13C-glucose uptake. Taurine utilization was confined to bacteria, whereas methionine was degraded by bacteria and archaea, including methanogenic Methanococcoides. Globally widespread uncultivated clades of Gammaproteobacteria and Deltaproteobacteria were the main drivers of DOS cycling and exhibited increased assimilation of carbon from taurine and methionine, compared to glucose. Only one operational taxonomic unit (OTU) affiliated with Neptuniibacter was found to assimilate taurine and methionine, but not glucose, implying that microbes exclusively utilizing both DOS substrates as a carbon source in marine sediments are rare. Still, a substantial number of bacterial taxa exhibited a higher assimilation of 13C from taurine or methionine, compared to glucose, indicating their preference for both DOS substrates over glucose as a carbon source in the sediment. These results represent the first quantitative assessment of organosulfur cycling from taurine and methionine by uncultivated microbes in a marine benthic environment.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf033"},"PeriodicalIF":5.1,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11905757/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143626819","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

Unraveling the impact of marine heatwaves on the Eukaryome of the emblematic Mediterranean red coral Corallium rubrum. 揭示海洋热浪对地中海红珊瑚（Corallium rubrum）真核体的影响

IF 5.1

ISME communications Pub Date : 2025-02-21 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf035

Camille Prioux, Christine Ferrier-Pagès, Javier Del Campo, Laure Guillou, Tristan Estaque, Denis Allemand, Romie Tignat-Perrier

{"title":"Unraveling the impact of marine heatwaves on the Eukaryome of the emblematic Mediterranean red coral Corallium rubrum.","authors":"Camille Prioux, Christine Ferrier-Pagès, Javier Del Campo, Laure Guillou, Tristan Estaque, Denis Allemand, Romie Tignat-Perrier","doi":"10.1093/ismeco/ycaf035","DOIUrl":"10.1093/ismeco/ycaf035","url":null,"abstract":"Global warming is intensifying heatwaves worldwide, leading to more frequent and severe temperature extremes. This study investigates the impact of the unprecedented 2022 Mediterranean heatwaves on the coral eukaryome, which has received little attention despite its known importance to coral holobiont functioning. Fifty-six colonies of the iconic red coral Corallium rubrum from the Mediterranean Sea were collected at different sites, depths, and health states. The microeukaryotic communities were analyzed using an 18S rRNA gene metabarcoding approach. Primers were designed to reduce amplification of the 18S rRNA gene sequences of the red coral while being universal for amplification of microeukaryotes. Our results showed that the red coral eukaryome was dominated by Dino-Group I, Licnophoridae, and Labyrinthulomycetes in the control sites that were not affected by the heat waves. In the heat-affected colonies, the composition of the coral eukaryome changed, with the relative abundances of Ephelotidae, Exobasidiomycetes, Corallicolidae, Labyrinthulomycetes, and/or the epibionts Phaeophyceae increasing depending on the intensity of heat stress experienced by the colonies. It was thus possible to link colony health to changes in the eukaryome. Finally, we illustrated putative interactions (competition, predator-prey relationship, and parasitism) occurring within C. rubrum eukaryome that could explain the compositional changes observed in the microeukaryotic communities under heat stress. Our findings improve our understanding of the ecological effects of heatwaves on marine ecosystems.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf035"},"PeriodicalIF":5.1,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11894933/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143607359","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