ISME communications最新文献

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Ferrihydrite-mediated methanotrophic nitrogen fixation in paddy soil under hypoxia. 缺氧条件下水稻田土壤中铁酸盐介导的甲烷固氮作用
ISME communications Pub Date : 2024-03-04 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae030
Linpeng Yu, Rong Jia, Shiqi Liu, Shuan Li, Sining Zhong, Guohong Liu, Raymond Jianxiong Zeng, Christopher Rensing, Shungui Zhou
{"title":"Ferrihydrite-mediated methanotrophic nitrogen fixation in paddy soil under hypoxia.","authors":"Linpeng Yu, Rong Jia, Shiqi Liu, Shuan Li, Sining Zhong, Guohong Liu, Raymond Jianxiong Zeng, Christopher Rensing, Shungui Zhou","doi":"10.1093/ismeco/ycae030","DOIUrl":"10.1093/ismeco/ycae030","url":null,"abstract":"<p><p>Biological nitrogen fixation (BNF) by methanotrophic bacteria has been shown to play an important role in maintaining fertility. However, this process is still limited to aerobic methane oxidation with sufficient oxygen. It has remained unknown whether and how methanotrophic BNF proceeds in hypoxic environments. Herein, we incubated paddy soils with a ferrihydrite-containing mineral salt medium to enrich methanotrophic bacteria in the presence of methane (20%, v/v) under oxygen constraints (0.27%, v/v). The resulting microcosms showed that ferrihydrite-dependent aerobic methane oxidation significantly contributed (81%) to total BNF, increasing the <sup>15</sup>N fixation rate by 13-fold from 0.02 to 0.28 μmol <sup>15</sup>N<sub>2</sub> (g dry weight soil) <sup>-1</sup> d<sup>-1</sup>. BNF was reduced by 97% when ferrihydrite was omitted, demonstrating the involvement of ferrihydrite in methanotrophic BNF. DNA stable-isotope probing indicated that <i>Methylocystis</i>, <i>Methylophilaceae</i>, and <i>Methylomicrobium</i> were the dominant methanotrophs/methylotrophs that assimilated labeled isotopes (<sup>13</sup>C or <sup>15</sup>N) into biomass. Metagenomic binning combined with electrochemical analysis suggested that <i>Methylocystis</i> and <i>Methylophilaceae</i> had the potential to perform methane-induced BNF and likely utilized riboflavin and <i>c</i>-type cytochromes as electron carriers for ferrihydrite reduction. It was concluded that ferrihydrite mediated methanotrophic BNF by methanotrophs/methylotrophs solely or in conjunction with iron-reducing bacteria. Overall, this study revealed a previously overlooked yet pronounced coupling of iron-dependent aerobic methane oxidation to BNF and improves our understanding of methanotrophic BNF in hypoxic zones.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae030"},"PeriodicalIF":0.0,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10960957/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140208854","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
Bacterial diversity and chemical ecology of natural product-producing bacteria from Great Salt Lake sediment. 大盐湖沉积物中产生天然产物的细菌多样性和化学生态学。
ISME communications Pub Date : 2024-03-04 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae029
Elijah R Bring Horvath, William J Brazelton, Min Cheol Kim, Reiko Cullum, Matthew A Mulvey, William Fenical, Jaclyn M Winter
{"title":"Bacterial diversity and chemical ecology of natural product-producing bacteria from Great Salt Lake sediment.","authors":"Elijah R Bring Horvath, William J Brazelton, Min Cheol Kim, Reiko Cullum, Matthew A Mulvey, William Fenical, Jaclyn M Winter","doi":"10.1093/ismeco/ycae029","DOIUrl":"10.1093/ismeco/ycae029","url":null,"abstract":"<p><p>Great Salt Lake (GSL), located northwest of Salt Lake City, UT, is the largest terminal lake in the USA. While the average salinity of seawater is ~3.3%, the salinity in GSL ranges between 5% and 28%. In addition to being a hypersaline environment, GSL also contains toxic concentrations of heavy metals, such as arsenic, mercury, and lead. The extreme environment of GSL makes it an intriguing subject of study, both for its unique microbiome and its potential to harbor novel natural product-producing bacteria, which could be used as resources for the discovery of biologically active compounds. Though work has been done to survey and catalog bacteria found in GSL, the Lake's microbiome is largely unexplored, and little to no work has been done to characterize the natural product potential of GSL microbes. Here, we investigate the bacterial diversity of two important regions within GSL, describe the first genomic characterization of Actinomycetota isolated from GSL sediment, including the identification of two new Actinomycetota species, and provide the first survey of the natural product potential of GSL bacteria.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae029"},"PeriodicalIF":0.0,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10960970/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140208424","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
Methylomonadaceae was the active and dominant methanotroph in Tibet lake sediments. 甲单胞菌是西藏湖泊沉积物中活跃的优势甲烷营养体。
ISME communications Pub Date : 2024-03-04 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae032
Yongcui Deng, Chulin Liang, Xiaomeng Zhu, Xinshu Zhu, Lei Chen, Hongan Pan, Fan Xun, Ye Tao, Peng Xing
{"title":"<i>Methylomonadaceae</i> was the active and dominant methanotroph in Tibet lake sediments.","authors":"Yongcui Deng, Chulin Liang, Xiaomeng Zhu, Xinshu Zhu, Lei Chen, Hongan Pan, Fan Xun, Ye Tao, Peng Xing","doi":"10.1093/ismeco/ycae032","DOIUrl":"10.1093/ismeco/ycae032","url":null,"abstract":"<p><p>Methane (CH<sub>4</sub>), an important greenhouse gas, significantly impacts the local and global climate. Our study focused on the composition and activity of methanotrophs residing in the lakes on the Tibetan Plateau, a hotspot for climate change research. Based on the field survey, the family <i>Methylomonadaceae</i> had a much higher relative abundance in freshwater lakes than in brackish and saline lakes, accounting for ~92% of total aerobic methanotrophs. Using the microcosm sediment incubation with <sup>13</sup>CH<sub>4</sub> followed by high throughput sequencing and metagenomic analysis, we further demonstrated that the family <i>Methylomonadaceae</i> was actively oxidizing CH<sub>4</sub>. Moreover, various methylotrophs, such as the genera <i>Methylotenera</i> and <i>Methylophilus</i>, were detected in the <sup>13</sup>C-labeled DNAs, which suggested their participation in CH<sub>4</sub>-carbon sequential assimilation. The presence of CH<sub>4</sub> metabolism, such as the tetrahydromethanopterin and the ribulose monophosphate pathways, was identified in the metagenome-assembled genomes of the family <i>Methylomonadaceae</i>. Furthermore, they had the potential to adapt to oxygen-deficient conditions and utilize multiple electron acceptors, such as metal oxides (Fe<sup>3+</sup>), nitrate, and nitrite, for survival in the Tibet lakes. Our findings highlighted the predominance of <i>Methylomonadaceae</i> and the associated microbes as active CH<sub>4</sub> consumers, potentially regulating the CH<sub>4</sub> emissions in the Tibet freshwater lakes. These insights contributed to understanding the plateau carbon cycle and emphasized the significance of methanotrophs in mitigating climate change.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae032"},"PeriodicalIF":0.0,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10960969/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140208423","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
Biotic interactions explain seasonal dynamics of the alpine soil microbiome. 生物相互作用解释了高山土壤微生物群的季节动态。
ISME communications Pub Date : 2024-02-28 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae028
Anna Maria Fiore-Donno, Jule Freudenthal, Mathilde Borg Dahl, Christian Rixen, Tim Urich, Michael Bonkowski
{"title":"Biotic interactions explain seasonal dynamics of the alpine soil microbiome.","authors":"Anna Maria Fiore-Donno, Jule Freudenthal, Mathilde Borg Dahl, Christian Rixen, Tim Urich, Michael Bonkowski","doi":"10.1093/ismeco/ycae028","DOIUrl":"10.1093/ismeco/ycae028","url":null,"abstract":"<p><p>While it is acknowledged that alpine soil bacterial communities are primarily driven by season and elevation, there is no consensus on the factors influencing fungi and protists. Here we used a holistic approach of the microbiome to investigate the seasonal dynamics in alpine grasslands, focusing on soil food web interactions. We collected 158 soil samples along elevation transects from three mountains in the Alps, in spring during snowmelt and in the following summer. Using metatranscriptomics, we simultaneously assessed prokaryotic and eukaryotic communities, further classified into trophic guilds. Our findings reveal that the consumers' pressure increases from spring to summer, leading to more diverse and evenly distributed prey communities. Consequently, consumers effectively maintain the diverse soil bacterial and fungal communities essential for ecosystem functioning. Our research highlights the significance of biotic interactions in understanding the distribution and dynamics of alpine microbial communities.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae028"},"PeriodicalIF":0.0,"publicationDate":"2024-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10945362/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140159720","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
Sea-ice melt determines seasonal phytoplankton dynamics and delimits the habitat of temperate Atlantic taxa as the Arctic Ocean atlantifies. 海冰融化决定了浮游植物的季节性动态,并随着北冰洋大陆化而划定了大西洋温带类群的栖息地。
ISME communications Pub Date : 2024-02-27 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae027
Ellen Oldenburg, Ovidiu Popa, Matthias Wietz, Wilken-Jon von Appen, Sinhue Torres-Valdes, Christina Bienhold, Oliver Ebenhöh, Katja Metfies
{"title":"Sea-ice melt determines seasonal phytoplankton dynamics and delimits the habitat of temperate Atlantic taxa as the Arctic Ocean atlantifies.","authors":"Ellen Oldenburg, Ovidiu Popa, Matthias Wietz, Wilken-Jon von Appen, Sinhue Torres-Valdes, Christina Bienhold, Oliver Ebenhöh, Katja Metfies","doi":"10.1093/ismeco/ycae027","DOIUrl":"10.1093/ismeco/ycae027","url":null,"abstract":"<p><p>The Arctic Ocean is one of the regions where anthropogenic environmental change is progressing most rapidly and drastically. The impact of rising temperatures and decreasing sea ice on Arctic marine microbial communities is yet not well understood. Microbes form the basis of food webs in the Arctic Ocean, providing energy for larger organisms. Previous studies have shown that Atlantic taxa associated with low light are robust to more polar conditions. We compared to which extent sea ice melt influences light-associated phytoplankton dynamics and biodiversity over two years at two mooring locations in the Fram Strait. One mooring is deployed in pure Atlantic water, and the second in the intermittently ice-covered Marginal Ice Zone. Time-series analysis of amplicon sequence variants abundance over a 2-year period, allowed us to identify communities of co-occurring taxa that exhibit similar patterns throughout the annual cycle. We then examined how alterations in environmental conditions affect the prevalence of species. During high abundance periods of diatoms, polar phytoplankton populations dominated, while temperate taxa were weakly represented. Furthermore, we found that polar pelagic and ice-associated taxa, such as <i>Fragilariopsis cylindrus</i> and <i>Melosira arctica</i>, were more common in Atlantic conditions, while temperate taxa, such as <i>Odontella aurita</i> and <i>Proboscia alata</i>, were less abundant under polar conditions. This suggests that sea ice melt may act as a barrier to the northward expansion of temperate phytoplankton, preventing their dominance in regions still strongly influenced by polar conditions. Our findings highlight the complex interactions between sea ice melt, phytoplankton dynamics, and biodiversity in the Arctic.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae027"},"PeriodicalIF":0.0,"publicationDate":"2024-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10955684/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140186475","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
Microeukaryotic plankton evolutionary constraints in a subtropical river explained by environment and bacteria along differing taxonomic resolutions. 亚热带河流中微真核浮游生物的进化制约因素可通过环境和细菌的不同分类分辨率来解释。
ISME communications Pub Date : 2024-02-24 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae026
Kexin Ren, Yuanyuan Mo, Peng Xiao, Regin Rønn, Zijie Xu, Yuanyuan Xue, Huihuang Chen, Windell L Rivera, Christopher Rensing, Jun Yang
{"title":"Microeukaryotic plankton evolutionary constraints in a subtropical river explained by environment and bacteria along differing taxonomic resolutions.","authors":"Kexin Ren, Yuanyuan Mo, Peng Xiao, Regin Rønn, Zijie Xu, Yuanyuan Xue, Huihuang Chen, Windell L Rivera, Christopher Rensing, Jun Yang","doi":"10.1093/ismeco/ycae026","DOIUrl":"10.1093/ismeco/ycae026","url":null,"abstract":"<p><p>Microeukaryotic plankton communities are keystone components for keeping aquatic primary productivity. Currently, variations in microeukaryotic plankton diversity have often been explained by local ecological factors but not by evolutionary constraints. We used amplicon sequencing of 100 water samples across five years to investigate the ecological preferences of the microeukaryotic plankton community in a subtropical riverine ecosystem. We found that microeukaryotic plankton diversity was less associated with bacterial abundance (16S rRNA gene copy number) than bacterial diversity. Further, environmental effects exhibited a larger influence on microeukaryotic plankton community composition than bacterial community composition, especially at fine taxonomic levels. The evolutionary constraints of microeukaryotic plankton community increased with decreasing taxonomic resolution (from 97% to 91% similarity levels), but not significant change from 85% to 70% similarity levels. However, compared with the bacterial community, the evolutionary constraints were shown to be more affected by environmental variables. This study illustrated possible controlling environmental and bacterial drivers of microeukaryotic diversity and community assembly in a subtropical river, thereby indirectly reflecting on the quality status of the water environment by providing new clues on the microeukaryotic community assembly.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae026"},"PeriodicalIF":0.0,"publicationDate":"2024-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10980835/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140337900","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
Evaluation of multiple displacement amplification for metagenomic analysis of low biomass samples. 评估用于低生物量样本元基因组分析的多重位移扩增技术。
ISME communications Pub Date : 2024-02-12 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae024
Melody Cabrera Ospino, Katja Engel, Santiago Ruiz-Navas, W Jeffrey Binns, Andrew C Doxey, Josh D Neufeld
{"title":"Evaluation of multiple displacement amplification for metagenomic analysis of low biomass samples.","authors":"Melody Cabrera Ospino, Katja Engel, Santiago Ruiz-Navas, W Jeffrey Binns, Andrew C Doxey, Josh D Neufeld","doi":"10.1093/ismeco/ycae024","DOIUrl":"10.1093/ismeco/ycae024","url":null,"abstract":"<p><p>Combining multiple displacement amplification (MDA) with metagenomics enables the analysis of samples with extremely low DNA concentrations, making them suitable for high-throughput sequencing. Although amplification bias and nonspecific amplification have been reported from MDA-amplified samples, the impact of MDA on metagenomic datasets is not well understood. We compared three MDA methods (i.e. bulk MDA, emulsion MDA, and primase MDA) for metagenomic analysis of two DNA template concentrations (approx. 1 and 100 pg) derived from a microbial community standard \"mock community\" and two low biomass environmental samples (i.e. borehole fluid and groundwater). We assessed the impact of MDA on metagenome-based community composition, assembly quality, functional profiles, and binning. We found amplification bias against high GC content genomes but relatively low nonspecific amplification such as chimeras, artifacts, or contamination for all MDA methods. We observed MDA-associated representational bias for microbial community profiles, especially for low-input DNA and with the primase MDA method. Nevertheless, similar taxa were represented in MDA-amplified libraries to those of unamplified samples. The MDA libraries were highly fragmented, but similar functional profiles to the unamplified libraries were obtained for bulk MDA and emulsion MDA at higher DNA input and across these MDA libraries for the groundwater sample. Medium to low-quality bins were possible for the high input bulk MDA metagenomes for the most simple microbial communities, borehole fluid, and mock community. Although MDA-based amplification should be avoided, it can still reveal meaningful taxonomic and functional information from samples with extremely low DNA concentration where direct metagenomics is otherwise impossible.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae024"},"PeriodicalIF":0.0,"publicationDate":"2024-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10945365/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140159746","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
Does soil history decline in influencing the structure of bacterial communities of Brassica napus host plants across different growth stages? 不同生长阶段的土壤历史是否会影响油菜寄主植物细菌群落的结构?
ISME communications Pub Date : 2024-01-31 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae019
Andrew J C Blakney, Marc St-Arnaud, Mohamed Hijri
{"title":"Does soil history decline in influencing the structure of bacterial communities of <i>Brassica napus</i> host plants across different growth stages?","authors":"Andrew J C Blakney, Marc St-Arnaud, Mohamed Hijri","doi":"10.1093/ismeco/ycae019","DOIUrl":"10.1093/ismeco/ycae019","url":null,"abstract":"<p><p>Soil history has been shown to condition future rhizosphere microbial communities. However, previous experiments have also illustrated that mature, adult plants can \"re-write,\" or mask, different soil histories through host plant-soil community feedbacks. This leaves a knowledge gap concerning how soil history influences bacterial community structure across different growth stages. Thus, here we tested the hypothesis that previously established soil histories will decrease in influencing the structure of <i>Brassica napus</i> bacterial communities over the growing season. We used an on-going agricultural field experiment to establish three different soil histories, plots of monocrop canola (<i>B. napus</i>), or rotations of wheat-canola, or pea-barley-canola. During the following season, we repeatedly sampled the surrounding bulk soil, rhizosphere, and roots of the <i>B. napus</i> hosts at different growth stages-the initial seeding conditions, seedling, rosette, bolting, and flower-from all three soil history plots. We compared composition and diversity of the <i>B. napus</i> soil bacterial communities, as estimated using 16S rRNA gene metabarcoding, to identify any changes associated with soil history and growth stages. We found that soil history remained significant across each growth stage in structuring the bacterial bulk soil and rhizosphere communities, but not the bacterial root communities. This suggests that the host plant's capacity to \"re-write\" different soil histories may be quite limited as key components that constitute the soil history's identity remain present, such that the previously established soil history continues to impact the bacterial rhizosphere communities, but not the root communities. For agriculture, this highlights how previously established soil histories persist and may have important long-term consequences on future plant-microbe communities, including bacteria.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae019"},"PeriodicalIF":0.0,"publicationDate":"2024-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10944699/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140159745","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
Total metagenomes outperform viromes in recovering viral diversity from sulfuric soils. 在从硫化土壤中恢复病毒多样性方面,总元基因组优于病毒组。
ISME communications Pub Date : 2024-01-27 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae017
Li Bi, Ji-Zheng He, Hang-Wei Hu
{"title":"Total metagenomes outperform viromes in recovering viral diversity from sulfuric soils.","authors":"Li Bi, Ji-Zheng He, Hang-Wei Hu","doi":"10.1093/ismeco/ycae017","DOIUrl":"10.1093/ismeco/ycae017","url":null,"abstract":"<p><p>Recent metagenomic advancements have offered unprecedented insights into soil viral ecology. However, it remains a challenge to select the suitable metagenomic method for investigating soil viruses under different environmental conditions. Here, we assessed the performance of viral size-fraction metagenomes (viromes) and total metagenomes in capturing viral diversity from hypersulfidic soils with neutral pH and sulfuric soils with pH <3.3. Viromes effectively enhanced the sequencing coverage of viral genomes in both soil types. Viomes of hypersulfidic soils outperformed total metagenomes by recovering a significantly higher number of viral operational taxonomic units (vOTUs). However, total metagenomes of sulfuric soils recovered ~4.5 times more vOTUs than viromes on average. Altogether, our findings suggest that the choice between viromes and total metagenomes for studying soil viruses should be carefully considered based on the specific environmental conditions.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae017"},"PeriodicalIF":0.0,"publicationDate":"2024-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10936692/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140121501","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
Microbial phosphorus recycling in soil by intra- and extracellular mechanisms 通过细胞内和细胞外机制实现土壤中微生物磷的循环利用
ISME communications Pub Date : 2024-01-24 DOI: 10.1038/s43705-023-00340-7
Jie Chen, Han Xu, Jasmin Seven, Thomas Zilla, Michaela A. Dippold, Yakov Kuzyakov
{"title":"Microbial phosphorus recycling in soil by intra- and extracellular mechanisms","authors":"Jie Chen,&nbsp;Han Xu,&nbsp;Jasmin Seven,&nbsp;Thomas Zilla,&nbsp;Michaela A. Dippold,&nbsp;Yakov Kuzyakov","doi":"10.1038/s43705-023-00340-7","DOIUrl":"10.1038/s43705-023-00340-7","url":null,"abstract":"Rising global stoichiometric imbalance between increasing nitrogen (N) availability and depleting phosphorus (P) resources increases the importance of soil microbial P recycling. The contribution of extra- versus intracellular P (re-)cycling depending on ecosystem nutrient status is vastly unclear, making soil microorganisms a blind spot in our understanding of ecosystem responses to increasing P deficiency. We quantified P incorporation into microbial DNA and phospholipids by 33P labeling under contrasting conditions: low/high P soil × low/high carbon (C)NP application.&nbsp;By combining 33P and 14C labeling with tracing of microbial community biomarkers and functional genes, we disengaged the role of DNA and phospholipids in soil P cycling. Microorganisms in low P soil preferentially allocated P to phospholipids with an acceleration of phospholipids metabolism driven by C addition,&nbsp;which was strongly related to high abundances of microbial community members (e.g. some G-) with a fast phospholipids turnover. In high P soil, however,&nbsp;more P was allocated to DNA with a microbial functional shift towards DNA synthesis to support a replicative growth when sufficient C was supplied, which was coupled with a strong enrichment of fungal copiotrophs and microbial genes coding DNA primase. Consequently, adaptation to low P availability accelerated microbial intracellular P recycling through reutilization of the P stored in phospholipids. However, microorganisms under high P availability commonly adopted extracellular P recycling with release and reuse of DNA P&nbsp;by microbial death-growth dynamics. These results advance our understanding on microbial adaptation to P deficiency in soil&nbsp;by regulating component-specific P pathways&nbsp;and reflect the specific functions of phospholipids and DNA for P recycling.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":" ","pages":"1-13"},"PeriodicalIF":0.0,"publicationDate":"2024-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s43705-023-00340-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139643975","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
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