Ying Jin, Wenkang Chen, Jie Hu, Jinfeng Wang, Hongqiang Ren
In wastewater treatment systems, the interactions among various microbes based on chemical signals, namely quorum sensing (QS), play critical roles in influencing microbial structure and function. However, it is challenging to understand the QS-controlled behaviors and the underlying mechanisms in complex microbial communities. In this study, we constructed a QS signaling network, providing insights into the intra- and interspecies interactions of activated sludge microbial communities based on diverse QS signal molecules. Our research underscores the role of diffusible signal factors (DSFs) in both intra- and interspecies communication among activated sludge microorganisms, and signal molecules commonly considered to mediate intraspecies communication may also participate in interspecies communication. QS signaling molecules play an important role as communal resources among the entire microbial group. The communication network within the microbial community is highly redundant, significantly contributing to the stability of natural microbial systems. This work contributes to the establishment of QS signaling network for activated sludge microbial communities, which may complement metabolic exchanges in explaining activated sludge microbial community structure and may help with a variety of future applications, such as making the dynamics and resilience of highly complex ecosystems more predictable.
{"title":"Constructions of quorum sensing Signaling network for activated sludge microbial community","authors":"Ying Jin, Wenkang Chen, Jie Hu, Jinfeng Wang, Hongqiang Ren","doi":"10.1093/ismeco/ycae018","DOIUrl":"https://doi.org/10.1093/ismeco/ycae018","url":null,"abstract":"\u0000 In wastewater treatment systems, the interactions among various microbes based on chemical signals, namely quorum sensing (QS), play critical roles in influencing microbial structure and function. However, it is challenging to understand the QS-controlled behaviors and the underlying mechanisms in complex microbial communities. In this study, we constructed a QS signaling network, providing insights into the intra- and interspecies interactions of activated sludge microbial communities based on diverse QS signal molecules. Our research underscores the role of diffusible signal factors (DSFs) in both intra- and interspecies communication among activated sludge microorganisms, and signal molecules commonly considered to mediate intraspecies communication may also participate in interspecies communication. QS signaling molecules play an important role as communal resources among the entire microbial group. The communication network within the microbial community is highly redundant, significantly contributing to the stability of natural microbial systems. This work contributes to the establishment of QS signaling network for activated sludge microbial communities, which may complement metabolic exchanges in explaining activated sludge microbial community structure and may help with a variety of future applications, such as making the dynamics and resilience of highly complex ecosystems more predictable.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139592927","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lukas Dreyling, C. Penone, Noelle Schenk, I. Schmitt, Francesco Dal Grande
Bark surfaces are extensive areas within forest ecosystems, that provide an ideal habitat for microbial communities, through their longevity and seasonal stability. Here we provide a comprehensive account of the bark surface microbiome of living trees in Central European forests, and identify drivers of diversity and community composition. We examine algal, fungal and bacterial communities and their interactions using metabarcoding on samples from over 750 trees collected in the Biodiversity Exploratories in northern, central and southern Germany. We show that mutual biotic influence is more important than the abiotic environment with regard to community composition, whereas abiotic conditions and geography are more important for alpha diversity. Important abiotic factors are the relative humidity and light availability, which decrease the algal and bacterial alpha diversity, but strongly increase fungal alpha diversity. In addition, temperature is important in shaping the microbial community, with higher temperature leading to homogeneous communities of dominant fungi, but high turnover in bacterial communities. Changes in the community dissimilarity of one organismal group occurs in close relation to changes in the other two, suggesting that there are close interactions between the three major groups of the bark surface microbial communities, which may be linked to beneficial exchange. To understand the functioning of the forest microbiome as a whole, we need to further investigate the functionality of interactions within the bark surface microbiome and combine these results with findings from other forest habitats such as soil or canopy.
{"title":"Biotic interactions outweigh abiotic factors as drivers of bark microbial communities in central European forests","authors":"Lukas Dreyling, C. Penone, Noelle Schenk, I. Schmitt, Francesco Dal Grande","doi":"10.1093/ismeco/ycae012","DOIUrl":"https://doi.org/10.1093/ismeco/ycae012","url":null,"abstract":"\u0000 Bark surfaces are extensive areas within forest ecosystems, that provide an ideal habitat for microbial communities, through their longevity and seasonal stability. Here we provide a comprehensive account of the bark surface microbiome of living trees in Central European forests, and identify drivers of diversity and community composition. We examine algal, fungal and bacterial communities and their interactions using metabarcoding on samples from over 750 trees collected in the Biodiversity Exploratories in northern, central and southern Germany. We show that mutual biotic influence is more important than the abiotic environment with regard to community composition, whereas abiotic conditions and geography are more important for alpha diversity. Important abiotic factors are the relative humidity and light availability, which decrease the algal and bacterial alpha diversity, but strongly increase fungal alpha diversity. In addition, temperature is important in shaping the microbial community, with higher temperature leading to homogeneous communities of dominant fungi, but high turnover in bacterial communities. Changes in the community dissimilarity of one organismal group occurs in close relation to changes in the other two, suggesting that there are close interactions between the three major groups of the bark surface microbial communities, which may be linked to beneficial exchange. To understand the functioning of the forest microbiome as a whole, we need to further investigate the functionality of interactions within the bark surface microbiome and combine these results with findings from other forest habitats such as soil or canopy.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139598394","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ying Zhang, Zhi-dong Li, Yuan Peng, Zimu Guo, Hong Wang, Tao Wei, Y. Shakir, Guohua Jiang, Yulin Deng
Dead-corner areas in space station that untouched by the clean-up campaign often experience microorganisms outbreaks, but the microbiome of these areas has never been studied. In this study, the microbiome in a ground-based analog “Tianhe” core module of China Space Station (CSS) was first investigated during a 50-day three-crew occupation. Dead-corner areas were receiving attention by adopting a new sampling method. Results indicate that the astronauts occupation did not affect the dominant bacteria community, but affected a small proportion. Due to the frequent activity of astronauts in the work and sleep areas, the biomarkers in these two areas are common human skin surface and gut microorganisms, respectively. For areas that astronauts rarely visit, the biomarkers in which are common environmental microbial groups. Fluorescence counting showed that 70.12–84.78% of bacteria were alive，with a quantity of 104–105 cells/100 cm2. With the occupation time extension, the number of microorganisms increased. At the same sampling time, there was no significant bioburden difference in various locations. The cultivable bioburden ranged from 101 to 104 CFU/100 cm2, which are the following 8 genera Penicillium, Microsphaeropsis, Stachybotrys, Humicola, Cladosporium, Bacillus, Planomicrobium and Acinetobacter. Chryseomicrobium genus may be a key focus for future microbial prevention and control work.
{"title":"Microbiome in a ground-based analog cabin of China Space Station during a 50-day human occupation","authors":"Ying Zhang, Zhi-dong Li, Yuan Peng, Zimu Guo, Hong Wang, Tao Wei, Y. Shakir, Guohua Jiang, Yulin Deng","doi":"10.1093/ismeco/ycae013","DOIUrl":"https://doi.org/10.1093/ismeco/ycae013","url":null,"abstract":"\u0000 Dead-corner areas in space station that untouched by the clean-up campaign often experience microorganisms outbreaks, but the microbiome of these areas has never been studied. In this study, the microbiome in a ground-based analog “Tianhe” core module of China Space Station (CSS) was first investigated during a 50-day three-crew occupation. Dead-corner areas were receiving attention by adopting a new sampling method. Results indicate that the astronauts occupation did not affect the dominant bacteria community, but affected a small proportion. Due to the frequent activity of astronauts in the work and sleep areas, the biomarkers in these two areas are common human skin surface and gut microorganisms, respectively. For areas that astronauts rarely visit, the biomarkers in which are common environmental microbial groups. Fluorescence counting showed that 70.12–84.78% of bacteria were alive，with a quantity of 104–105 cells/100 cm2. With the occupation time extension, the number of microorganisms increased. At the same sampling time, there was no significant bioburden difference in various locations. The cultivable bioburden ranged from 101 to 104 CFU/100 cm2, which are the following 8 genera Penicillium, Microsphaeropsis, Stachybotrys, Humicola, Cladosporium, Bacillus, Planomicrobium and Acinetobacter. Chryseomicrobium genus may be a key focus for future microbial prevention and control work.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139599792","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-01-24DOI: 10.1038/s43705-023-00340-7
Jie Chen, Han Xu, Jasmin Seven, Thomas Zilla, Michaela A. Dippold, Yakov Kuzyakov
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. 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, 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, 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 by microbial death-growth dynamics. These results advance our understanding on microbial adaptation to P deficiency in soil by regulating component-specific P pathways and reflect the specific functions of phospholipids and DNA for P recycling.
全球氮（N）供应量不断增加，而磷（P）资源却日益枯竭，这两者之间日益加剧的化学计量失衡增加了土壤微生物P循环的重要性。目前还不清楚生态系统养分状况对细胞外和胞内磷（再）循环的贡献，这使土壤微生物成为我们了解生态系统对日益严重的磷缺乏反应的一个盲点。通过 33P 和 14C 标记与微生物群落生物标志物和功能基因追踪相结合，我们揭示了 DNA 和磷脂在土壤磷循环中的作用。低磷土壤中的微生物优先将磷分配给磷脂，在C添加的驱动下加速磷脂代谢，这与磷脂周转快的高丰度微生物群落成员（如一些G-）密切相关。然而，在高磷土壤中，更多的磷被分配到 DNA 上，当提供充足的 C 时，微生物功能转向 DNA 合成，以支持复制生长，这与真菌共生菌和编码 DNA 引物酶的微生物基因的大量富集密切相关。因此，通过重新利用磷脂中储存的磷，对低磷供应的适应加速了微生物细胞内磷的循环。然而，在高P可用性条件下，微生物通常通过释放和再利用DNA P 通过微生物死亡-生长动力学来实现胞外P循环。这些结果加深了我们对微生物通过调节特定成分的钾途径来适应土壤钾缺乏的理解，并反映了磷脂和DNA在钾循环中的特定功能。
{"title":"Microbial phosphorus recycling in soil by intra- and extracellular mechanisms","authors":"Jie Chen, Han Xu, Jasmin Seven, Thomas Zilla, Michaela A. Dippold, 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. 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, 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, 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 by microbial death-growth dynamics. These results advance our understanding on microbial adaptation to P deficiency in soil by regulating component-specific P pathways and reflect the specific functions of phospholipids and DNA for P recycling.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":null,"pages":null},"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}
B. Rayamajhee, Mark Willcox, Savitri Sharma, Ronnie Mooney, Constantinos Petsoglou, Paul R Badenoch, S. Sherchan, Fiona L Henriquez, Nicole Carnt
Acanthamoeba, a free-living amoeba (FLA) in water and soil, is an emerging pathogen causing severe eye infections known as Acanthamoeba keratitis (AK). In its natural environment, Acanthamoeba performs a dual function as an environmental heterotrophic predator and host for a range of microorganisms that resist digestion. Our objective was to characterize the intracellular microorganisms of phylogenetically distinct Acanthamoeba spp. isolated in Australia and India through directly sequencing 16S rRNA amplicons from the amoebae. The presence of intracellular bacteria was further confirmed by in situ hybridization and electron microscopy. Among the 51 isolates assessed, 41% harboured intracellular bacteria which were clustered into four major phyla: Pseudomonadota (previously known as Proteobacteria), Bacteroidota (previously known as Bacteroidetes), Actinomycetota (previously known as Actinobacteria), and Bacillota (previously known as Firmicutes). The linear discriminate analysis effect size (LEfSe) analysis identified distinct microbial abundance patterns among the sample types; Pseudomonas species was abundant in Australian corneal isolates (p < 0.007), Enterobacteriales showed higher abundance in Indian corneal isolates (p < 0.017), and Bacteroidota was abundant in Australian water isolates (p < 0.019). The bacterial beta diversity of Acanthamoeba isolates from keratitis patients in India and Australia significantly differed (p < 0.05), while alpha diversity did not vary based on the country of origin or source of isolation (p > 0.05). More diverse intracellular bacteria were identified in water isolates as compared to clinical isolates. Confocal and electron microscopy confirmed the bacterial cells undergoing binary fission within the amoebal host, indicating the presence of viable bacteria. This study sheds light on the possibility of a sympatric lifestyle within Acanthamoeba, thereby emphasizing its crucial role as a bunker and carrier of potential human pathogens.
{"title":"Zooming in on the intracellular microbiome composition of bacterivorous Acanthamoeba isolates","authors":"B. Rayamajhee, Mark Willcox, Savitri Sharma, Ronnie Mooney, Constantinos Petsoglou, Paul R Badenoch, S. Sherchan, Fiona L Henriquez, Nicole Carnt","doi":"10.1093/ismeco/ycae016","DOIUrl":"https://doi.org/10.1093/ismeco/ycae016","url":null,"abstract":"\u0000 Acanthamoeba, a free-living amoeba (FLA) in water and soil, is an emerging pathogen causing severe eye infections known as Acanthamoeba keratitis (AK). In its natural environment, Acanthamoeba performs a dual function as an environmental heterotrophic predator and host for a range of microorganisms that resist digestion. Our objective was to characterize the intracellular microorganisms of phylogenetically distinct Acanthamoeba spp. isolated in Australia and India through directly sequencing 16S rRNA amplicons from the amoebae. The presence of intracellular bacteria was further confirmed by in situ hybridization and electron microscopy. Among the 51 isolates assessed, 41% harboured intracellular bacteria which were clustered into four major phyla: Pseudomonadota (previously known as Proteobacteria), Bacteroidota (previously known as Bacteroidetes), Actinomycetota (previously known as Actinobacteria), and Bacillota (previously known as Firmicutes). The linear discriminate analysis effect size (LEfSe) analysis identified distinct microbial abundance patterns among the sample types; Pseudomonas species was abundant in Australian corneal isolates (p < 0.007), Enterobacteriales showed higher abundance in Indian corneal isolates (p < 0.017), and Bacteroidota was abundant in Australian water isolates (p < 0.019). The bacterial beta diversity of Acanthamoeba isolates from keratitis patients in India and Australia significantly differed (p < 0.05), while alpha diversity did not vary based on the country of origin or source of isolation (p > 0.05). More diverse intracellular bacteria were identified in water isolates as compared to clinical isolates. Confocal and electron microscopy confirmed the bacterial cells undergoing binary fission within the amoebal host, indicating the presence of viable bacteria. This study sheds light on the possibility of a sympatric lifestyle within Acanthamoeba, thereby emphasizing its crucial role as a bunker and carrier of potential human pathogens.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139603465","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sean R Anderson, L. Blanco-Bercial, Craig A Carlson, Elizabeth L Harvey
Microbial associations that result in phytoplankton mortality are important for carbon transport in the ocean. This includes parasitism, which in microbial food webs is dominated by the marine alveolate group, Syndiniales. Parasites are expected to contribute to carbon recycling via host lysis; however, knowledge on host dynamics and correlation to carbon export remain unclear and limit the inclusion of parasitism in biogeochemical models. We analyzed a 4-year 18S rRNA gene metabarcoding dataset (2016–2019), performing network analysis for twelve discrete depths (1–1000 m) to determine Syndiniales-host associations in the seasonally oligotrophic Sargasso Sea. Analogous water column and sediment trap data were included to define environmental drivers of Syndiniales and their correlation with particulate carbon flux (150 m). Syndiniales accounted for 48–74% of network edges, most often associated with Dinophyceae and Arthropoda (mainly copepods) at the surface and Rhizaria (Polycystinea, Acantharea, and RAD-B) in the aphotic zone. Syndiniales were the only eukaryote group to be significantly (and negatively) correlated with particulate carbon flux, indicating their contribution to flux attenuation via remineralization. Examination of Syndiniales amplicons revealed a range of depth patterns, including specific ecological niches and vertical connection among a subset (19%) of the community, the latter implying sinking of parasites (infected hosts or spores) on particles. Our findings elevate the critical role of Syndiniales in marine microbial systems and reveal their potential use as biomarkers for carbon export.
{"title":"The role of Syndiniales parasites in depth-specific networks and carbon flux in the oligotrophic ocean","authors":"Sean R Anderson, L. Blanco-Bercial, Craig A Carlson, Elizabeth L Harvey","doi":"10.1093/ismeco/ycae014","DOIUrl":"https://doi.org/10.1093/ismeco/ycae014","url":null,"abstract":"\u0000 Microbial associations that result in phytoplankton mortality are important for carbon transport in the ocean. This includes parasitism, which in microbial food webs is dominated by the marine alveolate group, Syndiniales. Parasites are expected to contribute to carbon recycling via host lysis; however, knowledge on host dynamics and correlation to carbon export remain unclear and limit the inclusion of parasitism in biogeochemical models. We analyzed a 4-year 18S rRNA gene metabarcoding dataset (2016–2019), performing network analysis for twelve discrete depths (1–1000 m) to determine Syndiniales-host associations in the seasonally oligotrophic Sargasso Sea. Analogous water column and sediment trap data were included to define environmental drivers of Syndiniales and their correlation with particulate carbon flux (150 m). Syndiniales accounted for 48–74% of network edges, most often associated with Dinophyceae and Arthropoda (mainly copepods) at the surface and Rhizaria (Polycystinea, Acantharea, and RAD-B) in the aphotic zone. Syndiniales were the only eukaryote group to be significantly (and negatively) correlated with particulate carbon flux, indicating their contribution to flux attenuation via remineralization. Examination of Syndiniales amplicons revealed a range of depth patterns, including specific ecological niches and vertical connection among a subset (19%) of the community, the latter implying sinking of parasites (infected hosts or spores) on particles. Our findings elevate the critical role of Syndiniales in marine microbial systems and reveal their potential use as biomarkers for carbon export.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139605653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The effects of both bottom-up (e.g. substrate) and top-down (e.g. viral lysis) controls on the molecular composition of dissolved organic matter (DOM) have not been investigated. In this study, we investigated the DOM composition of the model bacterium Alteromonas macleodii ATCC 27126 growing on different substrates (glucose, laminarin, extracts from a Synechococcus culture, oligotrophic seawater and eutrophic seawater), and infected with a lytic phage. The ultra-high resolution mass spectrometry analysis showed that when growing on different substrates A. macleodii preferred to use reduced, saturated nitrogen-containing molecules (i.e. O4 formular species) and released or preserved oxidized, unsaturated sulfur-containing molecules (i.e. O7 formular species). However, when infected with the lytic phage, A. macleodii produced organic molecules with higher hydrogen saturation, and more nitrogen- or sulfur-containing molecules. Our results demonstrate that bottom-up (i.e. varying substrates) and top-down (i.e. viral lysis) controls leave different molecular fingerprints in the produced DOM.
自下而上（如基质）和自上而下（如病毒裂解）的控制对溶解有机物（DOM）分子组成的影响尚未得到研究。在本研究中，我们研究了生长在不同基质（葡萄糖、层糖蛋白、Synechococcus 培养物的提取物、低营养海水和富营养化海水）上并感染了溶菌噬菌体的模式菌 Alteromonas macleodii ATCC 27126 的 DOM 组成。超高分辨率质谱分析表明，当在不同基质上生长时，A. macleodii 喜欢使用还原的饱和含氮分子（即 O4 形式物种），并释放或保留氧化的不饱和含硫分子（即 O7 形式物种）。然而，当感染溶菌噬菌体时，A. macleodii 产生氢饱和度更高的有机分子，以及更多的含氮或含硫分子。我们的研究结果表明，自下而上（即不同的底物）和自上而下（即病毒裂解）的控制在产生的 DOM 中留下了不同的分子指纹。
{"title":"Bottom-up and top-down controls on Alteromonas macleodii lead to different dissolved organic matter compositions","authors":"Qi Chen, Christian Lønborg, Feng Chen, Rui Zhang, Ruanhong Cai, Yunyun Li, Chen He, Q. Shi, Nianzhi Jiao, Qiang Zheng","doi":"10.1093/ismeco/ycae010","DOIUrl":"https://doi.org/10.1093/ismeco/ycae010","url":null,"abstract":"\u0000 The effects of both bottom-up (e.g. substrate) and top-down (e.g. viral lysis) controls on the molecular composition of dissolved organic matter (DOM) have not been investigated. In this study, we investigated the DOM composition of the model bacterium Alteromonas macleodii ATCC 27126 growing on different substrates (glucose, laminarin, extracts from a Synechococcus culture, oligotrophic seawater and eutrophic seawater), and infected with a lytic phage. The ultra-high resolution mass spectrometry analysis showed that when growing on different substrates A. macleodii preferred to use reduced, saturated nitrogen-containing molecules (i.e. O4 formular species) and released or preserved oxidized, unsaturated sulfur-containing molecules (i.e. O7 formular species). However, when infected with the lytic phage, A. macleodii produced organic molecules with higher hydrogen saturation, and more nitrogen- or sulfur-containing molecules. Our results demonstrate that bottom-up (i.e. varying substrates) and top-down (i.e. viral lysis) controls leave different molecular fingerprints in the produced DOM.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139604430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marta Sebastián, Caterina. R. Giner, Vanessa Balagué, M. Gómez‐Letona, R. Massana, R. Logares, Carlos M Duarte, J. Gasol
A persistent microbial seed bank is postulated to sustain the marine biosphere, and recent findings show that prokaryotic taxa present in the ocean’s surface dominate prokaryotic communities throughout the water column. Yet, environmental conditions exert a tight control on the activity of prokaryotes, and drastic changes in these conditions are known to occur from the surface to deep waters. The simultaneous characterization of the total (DNA) and active (i.e., with potential for protein synthesis, RNA) free-living communities in thirteen stations distributed across the tropical and subtropical global ocean allowed us to assess their change in structure and diversity along the water column. We observed that active communities were surprisingly more similar along the vertical gradient than total communities. Looking at the vertical connectivity of the active vs. the total communities, we found that taxa detected in the surface sometimes accounted for more than 75% of the active microbiome of bathypelagic waters (50% on average). These active taxa were generally rare in the surface, representing a small fraction of all the surface taxa. Our findings show that the drastic vertical change in environmental conditions leads to the inactivation and disappearance of a large proportion of surface taxa, but some surface-rare taxa remain active (that is with potential for protein synthesis) and dominate the bathypelagic active microbiome.
{"title":"The active free-living bathypelagic microbiome is largely dominated by rare surface taxa","authors":"Marta Sebastián, Caterina. R. Giner, Vanessa Balagué, M. Gómez‐Letona, R. Massana, R. Logares, Carlos M Duarte, J. Gasol","doi":"10.1093/ismeco/ycae015","DOIUrl":"https://doi.org/10.1093/ismeco/ycae015","url":null,"abstract":"\u0000 A persistent microbial seed bank is postulated to sustain the marine biosphere, and recent findings show that prokaryotic taxa present in the ocean’s surface dominate prokaryotic communities throughout the water column. Yet, environmental conditions exert a tight control on the activity of prokaryotes, and drastic changes in these conditions are known to occur from the surface to deep waters. The simultaneous characterization of the total (DNA) and active (i.e., with potential for protein synthesis, RNA) free-living communities in thirteen stations distributed across the tropical and subtropical global ocean allowed us to assess their change in structure and diversity along the water column. We observed that active communities were surprisingly more similar along the vertical gradient than total communities. Looking at the vertical connectivity of the active vs. the total communities, we found that taxa detected in the surface sometimes accounted for more than 75% of the active microbiome of bathypelagic waters (50% on average). These active taxa were generally rare in the surface, representing a small fraction of all the surface taxa. Our findings show that the drastic vertical change in environmental conditions leads to the inactivation and disappearance of a large proportion of surface taxa, but some surface-rare taxa remain active (that is with potential for protein synthesis) and dominate the bathypelagic active microbiome.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139603847","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Fluorescence in situ hybridization (FISH) and 16S rRNA gene amplicon sequencing are commonly used for microbial ecological analyses in biological enhanced phosphorus removal (EBPR) systems, the successful application of which was governed by the oligonucleotides used. We performed a systemic evaluation of commonly used probes/primers for known polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs). Most FISH probes showed blind spots and covered nontarget bacterial groups. Ca. Competibacter probes showed promising coverage and specificity. Those for Ca. Accumulibacter are desirable in coverage but targeted out-group bacteria, including Ca. Competibacter, Thauera, Dechlorosoma, and some polyphosphate-accumulating Cyanobacteria. Defluviicoccus probes are good in specificity but poor in coverage. Probes targeting Tetrasphaera or Dechloromonas showed low coverage and specificity. Specifically, DEMEF455, Bet135, and Dech453 for Dechloromonas covered Ca. Accumulibacter. Special attentions are needed when using these probes to resolve the PAO/GAO phenotype of Dechloromonas. Most species-specific probes for Ca. Accumulibacter, Ca. Lutibacillus, Ca. Phosphoribacter, and Tetrasphaera are highly specific. Overall, 1.4% Ca. Accumulibacter, 9.6% Ca. Competibacter, 43.3% Defluviicoccus, and 54.0% Dechloromonas in the MiDAS database were not covered by existing FISH probes. Different 16S rRNA amplicon primer sets showed distinct coverage of known PAOs and GAOs. None of them covered all members. Overall, 520F-802R and 515F-926R showed the most balanced coverage. All primers showed extremely low coverage of Microlunatus (below 36.0%), implying their probably overlooked roles in EBPR systems. A clear understanding of the strength and weaknesses of each probe and primer set is a premise for rational evaluation and interpretation of obtained community results.
{"title":"Blind spots of universal primers and specific FISH probes for functional microbe and community characterization in EBPR systems","authors":"Jing Yuan, Xuhan Deng, Xiaojing Xie, Liping Chen, Chaohai Wei, Chunhua Feng, Guanglei Qiu","doi":"10.1093/ismeco/ycae011","DOIUrl":"https://doi.org/10.1093/ismeco/ycae011","url":null,"abstract":"\u0000 Fluorescence in situ hybridization (FISH) and 16S rRNA gene amplicon sequencing are commonly used for microbial ecological analyses in biological enhanced phosphorus removal (EBPR) systems, the successful application of which was governed by the oligonucleotides used. We performed a systemic evaluation of commonly used probes/primers for known polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs). Most FISH probes showed blind spots and covered nontarget bacterial groups. Ca. Competibacter probes showed promising coverage and specificity. Those for Ca. Accumulibacter are desirable in coverage but targeted out-group bacteria, including Ca. Competibacter, Thauera, Dechlorosoma, and some polyphosphate-accumulating Cyanobacteria. Defluviicoccus probes are good in specificity but poor in coverage. Probes targeting Tetrasphaera or Dechloromonas showed low coverage and specificity. Specifically, DEMEF455, Bet135, and Dech453 for Dechloromonas covered Ca. Accumulibacter. Special attentions are needed when using these probes to resolve the PAO/GAO phenotype of Dechloromonas. Most species-specific probes for Ca. Accumulibacter, Ca. Lutibacillus, Ca. Phosphoribacter, and Tetrasphaera are highly specific. Overall, 1.4% Ca. Accumulibacter, 9.6% Ca. Competibacter, 43.3% Defluviicoccus, and 54.0% Dechloromonas in the MiDAS database were not covered by existing FISH probes. Different 16S rRNA amplicon primer sets showed distinct coverage of known PAOs and GAOs. None of them covered all members. Overall, 520F-802R and 515F-926R showed the most balanced coverage. All primers showed extremely low coverage of Microlunatus (below 36.0%), implying their probably overlooked roles in EBPR systems. A clear understanding of the strength and weaknesses of each probe and primer set is a premise for rational evaluation and interpretation of obtained community results.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139604608","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The structure of microbiomes is often classified into discrete or semi-discrete types potentially differing in community-scale functional profiles. Elucidating mechanisms that generate such “alternative states” of microbiome compositions has been one of the major challenges in ecology and microbiology. In a time-series analysis of experimental microbiomes, we here show that both deterministic and stochastic ecological processes drive divergence of alternative microbiome states. We introduced species-rich soil-derived microbiomes into eight types of culture media with 48 replicates, monitoring shifts in community compositions at six time points (8 media × 48 replicates × 6 time points = 2,304 community samples). We then confirmed that microbial community structure diverged into a few state types in each of the eight medium conditions as predicted in the presence of both deterministic and stochastic community processes. In other words, microbiome structure was differentiated into a small number of reproducible compositions under the same environment. This fact indicates not only the presence of selective forces leading to specific equilibria of community-scale resource use but also the influence of demographic drift (fluctuations) on the microbiome assembly. A reference-genome-based analysis further suggested that the observed alternative states differed in ecosystem-level functions. These findings will help us examine how microbiome structure and functions can be controlled by changing the “stability landscapes” of ecological community compositions.
{"title":"Deterministic and stochastic processes generating alternative states of microbiomes","authors":"Ibuki Hayashi, Hiroaki Fujita, Hirokazu Toju","doi":"10.1093/ismeco/ycae007","DOIUrl":"https://doi.org/10.1093/ismeco/ycae007","url":null,"abstract":"\u0000 The structure of microbiomes is often classified into discrete or semi-discrete types potentially differing in community-scale functional profiles. Elucidating mechanisms that generate such “alternative states” of microbiome compositions has been one of the major challenges in ecology and microbiology. In a time-series analysis of experimental microbiomes, we here show that both deterministic and stochastic ecological processes drive divergence of alternative microbiome states. We introduced species-rich soil-derived microbiomes into eight types of culture media with 48 replicates, monitoring shifts in community compositions at six time points (8 media × 48 replicates × 6 time points = 2,304 community samples). We then confirmed that microbial community structure diverged into a few state types in each of the eight medium conditions as predicted in the presence of both deterministic and stochastic community processes. In other words, microbiome structure was differentiated into a small number of reproducible compositions under the same environment. This fact indicates not only the presence of selective forces leading to specific equilibria of community-scale resource use but also the influence of demographic drift (fluctuations) on the microbiome assembly. A reference-genome-based analysis further suggested that the observed alternative states differed in ecosystem-level functions. These findings will help us examine how microbiome structure and functions can be controlled by changing the “stability landscapes” of ecological community compositions.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139607916","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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