首页 > 最新文献

Environmental Microbiome最新文献

英文 中文
Identification of potential microbial risk factors associated with fecal indicator exceedances at recreational beaches. 确定与休闲海滩粪便指标超标有关的潜在微生物风险因素。
IF 7.9 2区 环境科学与生态学 Q1 GENETICS & HEREDITY Pub Date : 2024-01-15 DOI: 10.1186/s40793-024-00547-8
Faizan Saleem, Enze Li, Thomas A Edge, Kevin L Tran, Herb E Schellhorn

Background: Fecal bacterial densities are proxy indicators of beach water quality, and beach posting decisions are made based on Beach Action Value (BAV) exceedances for a beach. However, these traditional beach monitoring methods do not reflect the full extent of microbial water quality changes associated with BAV exceedances at recreational beaches (including harmful cyanobacteria). This proof of concept study evaluates the potential of metagenomics for comprehensively assessing bacterial community changes associated with BAV exceedances compared to non-exceedances for two urban beaches and their adjacent river water sources.

Results: Compared to non-exceedance samples, BAV exceedance samples exhibited higher alpha diversity (diversity within the sample) that could be further differentiated into separate clusters (Beta-diversity). For Beach A, Cyanobacterial sequences (resolved as Microcystis and Pseudanabaena at genus level) were significantly more abundant in BAV non-exceedance samples. qPCR validation supported the Cyanobacterial abundance results from metagenomic analysis and also identified saxitoxin genes in 50% of the non-exceedance samples. Microcystis sp and saxitoxin gene sequences were more abundant on non-exceedance beach days (when fecal indicator data indicated the beach should be open for water recreational purposes). For BAV exceedance days, Fibrobacteres, Pseudomonas, Acinetobacter, and Clostridium sequences were significantly more abundant (and positively correlated with fecal indicator densities) for Beach A. For Beach B, Spirochaetes (resolved as Leptospira on genus level) Burkholderia and Vibrio sequences were significantly more abundant in BAV exceedance samples. Similar bacterial diversity and abundance trends were observed for river water sources compared to their associated beaches. Antibiotic Resistance Genes (ARGs) were also consistently detected at both beaches. However, we did not observe a significant difference or correlation in ARGs abundance between BAV exceedance and non-exceedance samples.

Conclusion: This study provides a more comprehensive analysis of bacterial community changes associated with BAV exceedances for recreational freshwater beaches. While there were increases in bacterial diversity and some taxa of potential human health concern associated with increased fecal indicator densities and BAV exceedances (e.g. Pseudomonas), metagenomics analyses also identified other taxa of potential human health concern (e.g. Microcystis) associated with lower fecal indicator densities and BAV non-exceedances days. This study can help develop more targeted beach monitoring strategies and beach-specific risk management approaches.

背景:粪便细菌密度是海滩水质的代用指标,海滩行动值(BAV)超标会影响海滩的张贴决定。然而,这些传统的海滩监测方法并不能全面反映与休闲海滩 BAV 值超标相关的微生物水质变化(包括有害蓝藻)。这项概念验证研究评估了元基因组学在全面评估与两个城市海滩及其邻近河流水源的 BAV 超标相关的细菌群落变化方面的潜力:与未超标样本相比,BAV 超标样本表现出更高的α多样性(样本内部的多样性),并可进一步区分为不同的群集(β多样性)。qPCR 验证支持了元基因组分析得出的蓝藻丰度结果,并在 50%的非超标样本中发现了沙西毒素基因。微囊藻和沙希毒素基因序列在非超标海滩日(排泄物指标数据表明海滩应开放供水上娱乐活动时)更为丰富。在 BAV 超标日,海滩 A 的纤维细菌、假单胞菌、醋氨曲霉和梭状芽孢杆菌序列明显较多(且与粪便指标密度呈正相关);在海滩 B,BAV 超标样本中螺毛菌(在属级上解析为钩端螺旋体)、伯克霍尔德氏菌和弧菌序列明显较多。与相关海滩相比,在河水水源中也观察到了类似的细菌多样性和丰度趋势。在这两个海滩上还持续检测到抗生素耐药基因 (ARG)。但是,我们没有观察到 BAV 超标样本与未超标样本之间在 ARGs 丰度方面存在明显差异或相关性:本研究对与淡水休闲海滩 BAV 超标相关的细菌群落变化进行了更全面的分析。虽然细菌多样性有所增加,一些与排泄物指标密度增加和 BAV 超标有关的潜在人类健康问题分类群(如假单胞菌)也有所增加,但元基因组学分析还发现了与排泄物指标密度降低和 BAV 非超标天数有关的其他潜在人类健康问题分类群(如微囊藻)。这项研究有助于制定更有针对性的海滩监测策略和海滩风险管理方法。
{"title":"Identification of potential microbial risk factors associated with fecal indicator exceedances at recreational beaches.","authors":"Faizan Saleem, Enze Li, Thomas A Edge, Kevin L Tran, Herb E Schellhorn","doi":"10.1186/s40793-024-00547-8","DOIUrl":"10.1186/s40793-024-00547-8","url":null,"abstract":"<p><strong>Background: </strong>Fecal bacterial densities are proxy indicators of beach water quality, and beach posting decisions are made based on Beach Action Value (BAV) exceedances for a beach. However, these traditional beach monitoring methods do not reflect the full extent of microbial water quality changes associated with BAV exceedances at recreational beaches (including harmful cyanobacteria). This proof of concept study evaluates the potential of metagenomics for comprehensively assessing bacterial community changes associated with BAV exceedances compared to non-exceedances for two urban beaches and their adjacent river water sources.</p><p><strong>Results: </strong>Compared to non-exceedance samples, BAV exceedance samples exhibited higher alpha diversity (diversity within the sample) that could be further differentiated into separate clusters (Beta-diversity). For Beach A, Cyanobacterial sequences (resolved as Microcystis and Pseudanabaena at genus level) were significantly more abundant in BAV non-exceedance samples. qPCR validation supported the Cyanobacterial abundance results from metagenomic analysis and also identified saxitoxin genes in 50% of the non-exceedance samples. Microcystis sp and saxitoxin gene sequences were more abundant on non-exceedance beach days (when fecal indicator data indicated the beach should be open for water recreational purposes). For BAV exceedance days, Fibrobacteres, Pseudomonas, Acinetobacter, and Clostridium sequences were significantly more abundant (and positively correlated with fecal indicator densities) for Beach A. For Beach B, Spirochaetes (resolved as Leptospira on genus level) Burkholderia and Vibrio sequences were significantly more abundant in BAV exceedance samples. Similar bacterial diversity and abundance trends were observed for river water sources compared to their associated beaches. Antibiotic Resistance Genes (ARGs) were also consistently detected at both beaches. However, we did not observe a significant difference or correlation in ARGs abundance between BAV exceedance and non-exceedance samples.</p><p><strong>Conclusion: </strong>This study provides a more comprehensive analysis of bacterial community changes associated with BAV exceedances for recreational freshwater beaches. While there were increases in bacterial diversity and some taxa of potential human health concern associated with increased fecal indicator densities and BAV exceedances (e.g. Pseudomonas), metagenomics analyses also identified other taxa of potential human health concern (e.g. Microcystis) associated with lower fecal indicator densities and BAV non-exceedances days. This study can help develop more targeted beach monitoring strategies and beach-specific risk management approaches.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"19 1","pages":"4"},"PeriodicalIF":7.9,"publicationDate":"2024-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10790499/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139472929","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Phytoplankton ecology in the early years of a boreal oil sands end pit lake. 北方油砂末端矿坑湖早期的浮游植物生态学。
IF 7.9 2区 环境科学与生态学 Q1 GENETICS & HEREDITY Pub Date : 2024-01-12 DOI: 10.1186/s40793-023-00544-3
Chantel C Furgason, Angela V Smirnova, Joel B Dacks, Peter F Dunfield

Background: Base Mine Lake (BML) is the first full-scale end pit lake for the oil sands mining industry in Canada. BML sequesters oil sands tailings under a freshwater cap and is intended to develop into a functional ecosystem that can be integrated into the local watershed. The first stage of successful reclamation requires the development of a phytoplankton community supporting a typical boreal lake food web. To assess the diversity and dynamics of the phytoplankton community in BML at this reclamation stage and to set a baseline for future monitoring, we examined the phytoplankton community in BML from 2016 through 2021 using molecular methods (targeting the 23S, 18S, and 16S rRNA genes) and microscopic methods. Nearby water bodies were used as controls for a freshwater environment and an active tailings pond.

Results: The phytoplankton community was made up of diverse bacteria and eukaryotes typical of a boreal lake. Microscopy and molecular data both identified a phytoplankton community comparable at the phylum level to that of natural boreal lakes, dominated by Chlorophyta, Cryptophyta, and Cyanophyta, with some Bacillariophyta, Ochrophyta, and Euglenophyta. Although many of the same genera were prominent in both BML and the control freshwater reservoir, there were differences at the species or ASV level. Total diversity in BML was also consistently lower than the control freshwater site, but consistently higher than the control tailings pond. The phytoplankton community composition in BML changed over the 5-year study period. Some taxa present in 2016-2019 (e.g., Choricystis) were no longer detected in 2021, while some dinophytes and haptophytes became detectable in small quantities starting in 2019-2021. Different quantification methods (qPCR analysis of 23S rRNA genes, and microscopic estimates of populations and total biomass) did not show a consistent directional trend in total phytoplankton over the 5-year study, nor was there any consistent increase in phytoplankton species diversity. The 5-year period was likely an insufficient time frame for detecting community trends, as phytoplankton communities are highly variable at the genus and species level.

Conclusions: BML supports a phytoplankton community composition somewhat unique from control sites (active tailings and freshwater lake) and is still changing over time. However, the most abundant genera are typical of natural boreal lakes and have the potential to support a complex aquatic food web, with many of its identified major phytoplankton constituents known to be primary producers in boreal lake environments.

背景:基底矿湖(BML)是加拿大油砂开采业的第一个全规模尾矿湖。BML 将油砂尾矿封存在淡水盖下,旨在发展成为一个可融入当地流域的功能性生态系统。成功填海的第一阶段需要发展浮游植物群落,以支持典型的北方湖泊食物网。为了评估 BML 浮游植物群落在填海阶段的多样性和动态,并为未来的监测设定基线,我们采用分子方法(针对 23S、18S 和 16S rRNA 基因)和显微镜方法,对 2016 年至 2021 年期间 BML 的浮游植物群落进行了检测。附近的水体被用作淡水环境和活性尾矿池的对照:结果:浮游植物群落由典型北方湖泊的多种细菌和真核生物组成。显微镜和分子数据都确定了浮游植物群落的门类水平与天然北方湖泊相当,以叶绿藻门、隐藻门和蓝藻门为主,还有一些芽孢杆菌门、赭石门和优绿藻门。虽然许多相同的属在 BML 和对照淡水水库中都很突出,但在物种或 ASV 水平上存在差异。BML 的总多样性也一直低于对照淡水库,但高于对照尾矿库。在为期 5 年的研究期间,BML 中的浮游植物群落组成发生了变化。2016-2019 年出现的一些分类群(如 Choricystis)在 2021 年不再被检测到,而一些二叶藻和七叶藻则从 2019-2021 年开始被少量检测到。不同的定量方法(23S rRNA 基因的 qPCR 分析以及种群和总生物量的显微估算)在 5 年的研究中并没有显示出浮游植物总量的一致方向性趋势,浮游植物物种多样性也没有一致的增加。由于浮游植物群落在属和种的水平上变化很大,因此 5 年的时间可能不足以检测群落趋势:结论:BML 支持的浮游植物群落组成与对照地点(活动尾矿和淡水湖)有些不同,并且仍在随时间变化。然而,最丰富的属是典型的天然北方湖泊,有可能支持一个复杂的水生食物网,其中许多已确定的主要浮游植物成分是北方湖泊环境中已知的初级生产者。
{"title":"Phytoplankton ecology in the early years of a boreal oil sands end pit lake.","authors":"Chantel C Furgason, Angela V Smirnova, Joel B Dacks, Peter F Dunfield","doi":"10.1186/s40793-023-00544-3","DOIUrl":"10.1186/s40793-023-00544-3","url":null,"abstract":"<p><strong>Background: </strong>Base Mine Lake (BML) is the first full-scale end pit lake for the oil sands mining industry in Canada. BML sequesters oil sands tailings under a freshwater cap and is intended to develop into a functional ecosystem that can be integrated into the local watershed. The first stage of successful reclamation requires the development of a phytoplankton community supporting a typical boreal lake food web. To assess the diversity and dynamics of the phytoplankton community in BML at this reclamation stage and to set a baseline for future monitoring, we examined the phytoplankton community in BML from 2016 through 2021 using molecular methods (targeting the 23S, 18S, and 16S rRNA genes) and microscopic methods. Nearby water bodies were used as controls for a freshwater environment and an active tailings pond.</p><p><strong>Results: </strong>The phytoplankton community was made up of diverse bacteria and eukaryotes typical of a boreal lake. Microscopy and molecular data both identified a phytoplankton community comparable at the phylum level to that of natural boreal lakes, dominated by Chlorophyta, Cryptophyta, and Cyanophyta, with some Bacillariophyta, Ochrophyta, and Euglenophyta. Although many of the same genera were prominent in both BML and the control freshwater reservoir, there were differences at the species or ASV level. Total diversity in BML was also consistently lower than the control freshwater site, but consistently higher than the control tailings pond. The phytoplankton community composition in BML changed over the 5-year study period. Some taxa present in 2016-2019 (e.g., Choricystis) were no longer detected in 2021, while some dinophytes and haptophytes became detectable in small quantities starting in 2019-2021. Different quantification methods (qPCR analysis of 23S rRNA genes, and microscopic estimates of populations and total biomass) did not show a consistent directional trend in total phytoplankton over the 5-year study, nor was there any consistent increase in phytoplankton species diversity. The 5-year period was likely an insufficient time frame for detecting community trends, as phytoplankton communities are highly variable at the genus and species level.</p><p><strong>Conclusions: </strong>BML supports a phytoplankton community composition somewhat unique from control sites (active tailings and freshwater lake) and is still changing over time. However, the most abundant genera are typical of natural boreal lakes and have the potential to support a complex aquatic food web, with many of its identified major phytoplankton constituents known to be primary producers in boreal lake environments.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"19 1","pages":"3"},"PeriodicalIF":7.9,"publicationDate":"2024-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10787447/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139432267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Selective regulation of endophytic bacteria and gene expression in soybean by water-soluble humic materials. 水溶性腐殖质对大豆内生菌和基因表达的选择性调控。
IF 7.9 2区 环境科学与生态学 Q1 GENETICS & HEREDITY Pub Date : 2024-01-04 DOI: 10.1186/s40793-023-00546-1
Wenqian Wang, Dongmei Li, Xiaoqian Qiu, Jinshui Yang, Liang Liu, Entao Wang, Hongli Yuan

Background: As part of the plant microbiome, endophytic bacteria play an essential role in plant growth and resistance to stress. Water-soluble humic materials (WSHM) is widely used in sustainable agriculture as a natural and non-polluting plant growth regulator to promote the growth of plants and beneficial bacteria. However, the mechanisms of WSHM to promote plant growth and the evidence for commensal endophytic bacteria interaction with their host remain largely unknown. Here, 16S rRNA gene sequencing, transcriptomic analysis, and culture-based methods were used to reveal the underlying mechanisms.

Results: WSHM reduced the alpha diversity of soybean endophytic bacteria, but increased the bacterial interactions and further selectively enriched the potentially beneficial bacteria. Meanwhile, WSHM regulated the expression of various genes related to the MAPK signaling pathway, plant-pathogen interaction, hormone signal transduction, and synthetic pathways in soybean root. Omics integration analysis showed that Sphingobium was the genus closest to the significantly changed genes in WSHM treatment. The inoculation of endophytic Sphingobium sp. TBBS4 isolated from soybean significantly improved soybean nodulation and growth by increasing della gene expression and reducing ethylene release.

Conclusion: All the results revealed that WSHM promotes soybean nodulation and growth by selectively regulating soybean gene expression and regulating the endophytic bacterial community, Sphingobium was the key bacterium involved in plant-microbe interaction. These findings refined our understanding of the mechanism of WSHM promoting soybean nodulation and growth and provided novel evidence for plant-endophyte interaction.

背景:作为植物微生物群的一部分,内生细菌在植物生长和抗逆方面发挥着至关重要的作用。水溶性腐殖质材料(WSHM)作为一种天然、无污染的植物生长调节剂,被广泛应用于可持续农业,以促进植物和有益菌的生长。然而,水溶性腐殖质促进植物生长的机制以及共生内生菌与其宿主相互作用的证据在很大程度上仍然未知。本文采用 16S rRNA 基因测序、转录组分析和基于培养的方法来揭示其潜在机制:结果:WSHM 降低了大豆内生菌的α-多样性,但增加了细菌间的相互作用,并进一步选择性地富集了潜在的有益细菌。同时,WSHM 调节了大豆根部与 MAPK 信号通路、植物与病原菌相互作用、激素信号转导和合成途径相关的各种基因的表达。Omics 整合分析表明,在 WSHM 处理中,与发生显著变化的基因最接近的属是鞘氨醇属。接种从大豆中分离的内生Sphingobium sp. TBBS4后,通过增加della基因的表达和减少乙烯的释放,大豆的结瘤和生长得到了明显改善:所有研究结果表明,WSHM 通过选择性调控大豆基因表达和内生细菌群落来促进大豆的结瘤和生长。这些发现完善了我们对 WSHM 促进大豆拔节和生长机制的认识,并为植物与内生菌的相互作用提供了新的证据。
{"title":"Selective regulation of endophytic bacteria and gene expression in soybean by water-soluble humic materials.","authors":"Wenqian Wang, Dongmei Li, Xiaoqian Qiu, Jinshui Yang, Liang Liu, Entao Wang, Hongli Yuan","doi":"10.1186/s40793-023-00546-1","DOIUrl":"10.1186/s40793-023-00546-1","url":null,"abstract":"<p><strong>Background: </strong>As part of the plant microbiome, endophytic bacteria play an essential role in plant growth and resistance to stress. Water-soluble humic materials (WSHM) is widely used in sustainable agriculture as a natural and non-polluting plant growth regulator to promote the growth of plants and beneficial bacteria. However, the mechanisms of WSHM to promote plant growth and the evidence for commensal endophytic bacteria interaction with their host remain largely unknown. Here, 16S rRNA gene sequencing, transcriptomic analysis, and culture-based methods were used to reveal the underlying mechanisms.</p><p><strong>Results: </strong>WSHM reduced the alpha diversity of soybean endophytic bacteria, but increased the bacterial interactions and further selectively enriched the potentially beneficial bacteria. Meanwhile, WSHM regulated the expression of various genes related to the MAPK signaling pathway, plant-pathogen interaction, hormone signal transduction, and synthetic pathways in soybean root. Omics integration analysis showed that Sphingobium was the genus closest to the significantly changed genes in WSHM treatment. The inoculation of endophytic Sphingobium sp. TBBS4 isolated from soybean significantly improved soybean nodulation and growth by increasing della gene expression and reducing ethylene release.</p><p><strong>Conclusion: </strong>All the results revealed that WSHM promotes soybean nodulation and growth by selectively regulating soybean gene expression and regulating the endophytic bacterial community, Sphingobium was the key bacterium involved in plant-microbe interaction. These findings refined our understanding of the mechanism of WSHM promoting soybean nodulation and growth and provided novel evidence for plant-endophyte interaction.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"19 1","pages":"2"},"PeriodicalIF":7.9,"publicationDate":"2024-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10768371/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139099033","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","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 unified compendium of prokaryotic and viral genomes from over 300 anaerobic digestion microbiomes 来自 300 多个厌氧消化微生物组的原核生物和病毒基因组统一汇编
IF 7.9 2区 环境科学与生态学 Q1 GENETICS & HEREDITY Pub Date : 2024-01-02 DOI: 10.1186/s40793-023-00545-2
Victor Borin Centurion, Alessandro Rossi, Esteban Orellana, Gabriele Ghiotto, Balázs Kakuk, Maria Silvia Morlino, Arianna Basile, Guido Zampieri, Laura Treu, Stefano Campanaro
The anaerobic digestion process degrades organic matter into simpler compounds and occurs in strictly anaerobic and microaerophilic environments. The process is carried out by a diverse community of microorganisms where each species has a unique role and it has relevant biotechnological applications since it is used for biogas production. Some aspects of the microbiome, including its interaction with phages, remains still unclear: a better comprehension of the community composition and role of each species is crucial for a cured understanding of the carbon cycle in anaerobic systems and improving biogas production. The primary objective of this study was to expand our understanding on the anaerobic digestion microbiome by jointly analyzing its prokaryotic and viral components. By integrating 192 additional datasets into a previous metagenomic database, the binning process generated 11,831 metagenome-assembled genomes from 314 metagenome samples published between 2014 and 2022, belonging to 4,568 non-redundant species based on ANI calculation and quality verification. CRISPR analysis on these genomes identified 76 archaeal genomes with active phage interactions. Moreover, single-nucleotide variants further pointed to archaea as the most critical members of the community. Among the MAGs, two methanogenic archaea, Methanothrix sp. 43zhSC_152 and Methanoculleus sp. 52maCN_3230, had the highest number of SNVs, with the latter having almost double the density of most other MAGs. This study offers a more comprehensive understanding of microbial community structures that thrive at different temperatures. The findings revealed that the fraction of archaeal species characterized at the genome level and reported in public databases is higher than that of bacteria, although still quite limited. The identification of shared spacers between phages and microbes implies a history of phage-bacterial interactions, and specifically lysogenic infections. A significant number of SNVs were identified, primarily comprising synonymous and nonsynonymous variants. Together, the findings indicate that methanogenic archaea are subject to intense selective pressure and suggest that genomic variants play a critical role in the anaerobic digestion process. Overall, this study provides a more balanced and diverse representation of the anaerobic digestion microbiota in terms of geographic location, temperature range and feedstock utilization.
厌氧消化过程将有机物降解为较简单的化合物,发生在严格厌氧和微嗜水的环境中。厌氧消化过程由多种多样的微生物群落进行,其中每个物种都有独特的作用,而且厌氧消化还具有相关的生物技术应用,因为它可用于生产沼气。微生物群的某些方面,包括其与噬菌体的相互作用,仍不清楚:更好地理解群落组成和每个物种的作用,对于深入了解厌氧系统中的碳循环和提高沼气产量至关重要。本研究的主要目的是通过联合分析厌氧消化微生物群的原核生物和病毒成分,扩大我们对厌氧消化微生物群的了解。通过将 192 个附加数据集整合到之前的元基因组数据库中,分选过程从 2014 年至 2022 年间发表的 314 个元基因组样本中生成了 11831 个元基因组组装基因组,根据 ANI 计算和质量验证,这些基因组属于 4568 个非冗余物种。对这些基因组进行的CRISPR分析发现了76个具有活跃噬菌体相互作用的古菌基因组。此外,单核苷酸变异进一步表明古菌是群落中最关键的成员。在这些噬菌体中,两个产甲烷古细菌--Methanothrix sp.(43zhSC_152)和 Methanoculleus sp.(52maCN_3230)--的 SNV 数量最多,其中后者的 SNV 密度几乎是大多数其他噬菌体的两倍。这项研究让人们对在不同温度下生长的微生物群落结构有了更全面的了解。研究结果表明,在基因组水平上表征并在公共数据库中报告的古细菌物种的比例高于细菌,但仍然相当有限。噬菌体与微生物之间共享间隔的发现意味着噬菌体与细菌之间存在相互作用的历史,特别是溶菌感染。研究发现了大量 SNVs,主要包括同义和非同义变异。这些发现共同表明,产甲烷古细菌承受着巨大的选择压力,并表明基因组变异在厌氧消化过程中发挥着关键作用。总之,这项研究从地理位置、温度范围和原料利用等方面提供了厌氧消化微生物群更加平衡和多样化的代表。
{"title":"A unified compendium of prokaryotic and viral genomes from over 300 anaerobic digestion microbiomes","authors":"Victor Borin Centurion, Alessandro Rossi, Esteban Orellana, Gabriele Ghiotto, Balázs Kakuk, Maria Silvia Morlino, Arianna Basile, Guido Zampieri, Laura Treu, Stefano Campanaro","doi":"10.1186/s40793-023-00545-2","DOIUrl":"https://doi.org/10.1186/s40793-023-00545-2","url":null,"abstract":"The anaerobic digestion process degrades organic matter into simpler compounds and occurs in strictly anaerobic and microaerophilic environments. The process is carried out by a diverse community of microorganisms where each species has a unique role and it has relevant biotechnological applications since it is used for biogas production. Some aspects of the microbiome, including its interaction with phages, remains still unclear: a better comprehension of the community composition and role of each species is crucial for a cured understanding of the carbon cycle in anaerobic systems and improving biogas production. The primary objective of this study was to expand our understanding on the anaerobic digestion microbiome by jointly analyzing its prokaryotic and viral components. By integrating 192 additional datasets into a previous metagenomic database, the binning process generated 11,831 metagenome-assembled genomes from 314 metagenome samples published between 2014 and 2022, belonging to 4,568 non-redundant species based on ANI calculation and quality verification. CRISPR analysis on these genomes identified 76 archaeal genomes with active phage interactions. Moreover, single-nucleotide variants further pointed to archaea as the most critical members of the community. Among the MAGs, two methanogenic archaea, Methanothrix sp. 43zhSC_152 and Methanoculleus sp. 52maCN_3230, had the highest number of SNVs, with the latter having almost double the density of most other MAGs. This study offers a more comprehensive understanding of microbial community structures that thrive at different temperatures. The findings revealed that the fraction of archaeal species characterized at the genome level and reported in public databases is higher than that of bacteria, although still quite limited. The identification of shared spacers between phages and microbes implies a history of phage-bacterial interactions, and specifically lysogenic infections. A significant number of SNVs were identified, primarily comprising synonymous and nonsynonymous variants. Together, the findings indicate that methanogenic archaea are subject to intense selective pressure and suggest that genomic variants play a critical role in the anaerobic digestion process. Overall, this study provides a more balanced and diverse representation of the anaerobic digestion microbiota in terms of geographic location, temperature range and feedstock utilization.","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"7 1","pages":""},"PeriodicalIF":7.9,"publicationDate":"2024-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139083011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Increased prokaryotic diversity in the Red Sea deep scattering layer 红海深散射层中原核生物多样性增加
IF 7.9 2区 环境科学与生态学 Q1 GENETICS & HEREDITY Pub Date : 2023-12-14 DOI: 10.1186/s40793-023-00542-5
Tamara Megan Huete-Stauffer, Ramiro Logares, Mohd Ikram Ansari, Anders Røstad, Maria Lluch Calleja, Xosé Anxelu G. Morán
The diel vertical migration (DVM) of fish provides an active transport of labile dissolved organic matter (DOM) to the deep ocean, fueling the metabolism of heterotrophic bacteria and archaea. We studied the impact of DVM on the mesopelagic prokaryotic diversity of the Red Sea focusing on the mesopelagic deep scattering layer (DSL) between 450–600 m. Despite the general consensus of homogeneous conditions in the mesopelagic layer, we observed variability in physico-chemical variables (oxygen, inorganic nutrients, DOC) in the depth profiles. We also identified distinct seasonal indicator prokaryotes inhabiting the DSL, representing between 2% (in spring) to over 10% (in winter) of total 16S rRNA gene sequences. The dominant indicator groups were Alteromonadales in winter, Vibrionales in spring and Microtrichales in summer. Using multidimensional scaling analysis, the DSL samples showed divergence from the surrounding mesopelagic layers and were distributed according to depth (47% of variance explained). We identified the sources of diversity that contribute to the DSL by analyzing the detailed profiles of spring, where 3 depths were sampled in the mesopelagic. On average, 7% was related to the epipelagic, 34% was common among the other mesopelagic waters and 38% was attributable to the DSL, with 21% of species being unique to this layer. We conclude that the mesopelagic physico-chemical properties shape a rather uniform prokaryotic community, but that the 200 m deep DSL contributes uniquely and in a high proportion to the diversity of the Red Sea mesopelagic.
鱼类的昼夜垂直洄游(DVM)将可溶性溶解有机物(DOM)主动输送到深海,促进了异养细菌和古细菌的新陈代谢。我们研究了 DVM 对红海中层原核生物多样性的影响,重点是 450-600 米之间的中层深散射层(DSL)。尽管普遍认为中层深散射层的条件是均匀的,但我们观察到深度剖面中物理化学变量(氧气、无机营养物质、溶解氧)的变化。我们还发现了栖息在 DSL 中不同季节的指示原核生物,占 16S rRNA 基因序列总数的 2%(春季)到 10%以上(冬季)。主要指标类群是冬季的 Alteromonadales、春季的 Vibrionales 和夏季的 Microtrichales。通过多维尺度分析,DSL 样本显示出与周围中深海层的差异,并按深度分布(47% 的方差解释)。我们通过分析春季的详细剖面图,确定了造成 DSL 的多样性来源。平均而言,7%的物种与上深层有关,34%的物种在其他中深层水域中常见,38%的物种可归因于DSL,其中21%的物种为该层所独有。我们的结论是,中层水的物理化学特性形成了一个相当统一的原核生物群落,但 200 米深的 DSL 对红海中层水的多样性做出了独特的贡献,而且比例很高。
{"title":"Increased prokaryotic diversity in the Red Sea deep scattering layer","authors":"Tamara Megan Huete-Stauffer, Ramiro Logares, Mohd Ikram Ansari, Anders Røstad, Maria Lluch Calleja, Xosé Anxelu G. Morán","doi":"10.1186/s40793-023-00542-5","DOIUrl":"https://doi.org/10.1186/s40793-023-00542-5","url":null,"abstract":"The diel vertical migration (DVM) of fish provides an active transport of labile dissolved organic matter (DOM) to the deep ocean, fueling the metabolism of heterotrophic bacteria and archaea. We studied the impact of DVM on the mesopelagic prokaryotic diversity of the Red Sea focusing on the mesopelagic deep scattering layer (DSL) between 450–600 m. Despite the general consensus of homogeneous conditions in the mesopelagic layer, we observed variability in physico-chemical variables (oxygen, inorganic nutrients, DOC) in the depth profiles. We also identified distinct seasonal indicator prokaryotes inhabiting the DSL, representing between 2% (in spring) to over 10% (in winter) of total 16S rRNA gene sequences. The dominant indicator groups were Alteromonadales in winter, Vibrionales in spring and Microtrichales in summer. Using multidimensional scaling analysis, the DSL samples showed divergence from the surrounding mesopelagic layers and were distributed according to depth (47% of variance explained). We identified the sources of diversity that contribute to the DSL by analyzing the detailed profiles of spring, where 3 depths were sampled in the mesopelagic. On average, 7% was related to the epipelagic, 34% was common among the other mesopelagic waters and 38% was attributable to the DSL, with 21% of species being unique to this layer. We conclude that the mesopelagic physico-chemical properties shape a rather uniform prokaryotic community, but that the 200 m deep DSL contributes uniquely and in a high proportion to the diversity of the Red Sea mesopelagic.","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"55 1","pages":""},"PeriodicalIF":7.9,"publicationDate":"2023-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138679725","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
DNA from non-viable bacteria biases diversity estimates in the corals Acropora loripes and Pocillopora acuta 来自无法存活的细菌的 DNA 使珊瑚 Acropora loripes 和 Pocillopora acuta 的多样性估计值出现偏差
IF 7.9 2区 环境科学与生态学 Q1 GENETICS & HEREDITY Pub Date : 2023-12-08 DOI: 10.1186/s40793-023-00541-6
Ashley M. Dungan, Laura Geissler, Amanda S. Williams, Cecilie Ravn Gotze, Emily C. Flynn, Linda L. Blackall, Madeleine J. H. van Oppen
Nucleic acid-based analytical methods have greatly expanded our understanding of global prokaryotic diversity, yet standard metabarcoding methods provide no information on the most fundamental physiological state of bacteria, viability. Scleractinian corals harbour a complex microbiome in which bacterial symbionts play critical roles in maintaining health and functioning of the holobiont. However, the coral holobiont contains both dead and living bacteria. The former can be the result of corals feeding on bacteria, rapid swings from hyper- to hypoxic conditions in the coral tissue, the presence of antimicrobial compounds in coral mucus, and an abundance of lytic bacteriophages. By combining propidium monoazide (PMA) treatment with high-throughput sequencing on six coral species (Acropora loripes, A. millepora, A. kenti, Platygyra daedalea, Pocillopora acuta, and Porites lutea) we were able to obtain information on bacterial communities with little noise from non-viable microbial DNA. Metabarcoding of the 16S rRNA gene showed significantly higher community evenness (85%) and species diversity (31%) in untreated compared with PMA-treated tissue for A. loripes only. While PMA-treated coral did not differ significantly from untreated samples in terms of observed number of ASVs, > 30% of ASVs were identified in untreated samples only, suggesting that they originated from cell-free/non-viable DNA. Further, the bacterial community structure was significantly different between PMA-treated and untreated samples for A. loripes and P. acuta indicating that DNA from non-viable microbes can bias community composition data in coral species with low bacterial diversity. Our study is highly relevant to microbiome studies on coral and other host organisms as it delivers a solution to excluding non-viable DNA in a complex community. These results provide novel insights into the dynamic nature of host-associated microbiomes and underline the importance of applying versatile tools in the analysis of metabarcoding or next-generation sequencing data sets.
基于核酸的分析方法极大地扩展了我们对全球原核生物多样性的了解,然而标准的代谢编码方法却无法提供细菌最基本的生理状态--生存能力的信息。硬骨鱼类珊瑚蕴藏着复杂的微生物群,其中的细菌共生体在维持整体生物的健康和功能方面发挥着至关重要的作用。然而,珊瑚全生物体中既有死细菌,也有活细菌。前者可能是珊瑚以细菌为食、珊瑚组织中从高氧到低氧条件快速波动、珊瑚粘液中存在抗菌化合物以及大量溶菌噬菌体的结果。通过在六个珊瑚物种(Acropora loripes、A. millepora、A. kenti、Platygyra daedalea、Pocillopora acuta 和 Porites lutea)上将单氮化丙啶(PMA)处理与高通量测序相结合,我们能够获得细菌群落的信息,而非存活微生物 DNA 的干扰很小。16S rRNA 基因的元条码显示,与 PMA 处理的组织相比,未处理的 A. loripes 的群落均匀度(85%)和物种多样性(31%)明显更高。虽然就观察到的 ASV 数量而言,PMA 处理过的珊瑚与未处理过的样本没有明显差异,但仅在未处理过的样本中发现了超过 30% 的 ASV,这表明它们来自无细胞/非存活 DNA。此外,对 A. loripes 和 P. acuta 而言,经 PMA 处理的样本与未经处理的样本之间的细菌群落结构存在显著差异,这表明在细菌多样性较低的珊瑚物种中,来自不可存活微生物的 DNA 可能会使群落组成数据出现偏差。我们的研究与珊瑚和其他宿主生物的微生物组研究高度相关,因为它提供了一种在复杂群落中排除非存活 DNA 的解决方案。这些结果为了解宿主相关微生物群的动态性质提供了新的视角,并强调了在分析代谢条码或新一代测序数据集时应用多功能工具的重要性。
{"title":"DNA from non-viable bacteria biases diversity estimates in the corals Acropora loripes and Pocillopora acuta","authors":"Ashley M. Dungan, Laura Geissler, Amanda S. Williams, Cecilie Ravn Gotze, Emily C. Flynn, Linda L. Blackall, Madeleine J. H. van Oppen","doi":"10.1186/s40793-023-00541-6","DOIUrl":"https://doi.org/10.1186/s40793-023-00541-6","url":null,"abstract":"Nucleic acid-based analytical methods have greatly expanded our understanding of global prokaryotic diversity, yet standard metabarcoding methods provide no information on the most fundamental physiological state of bacteria, viability. Scleractinian corals harbour a complex microbiome in which bacterial symbionts play critical roles in maintaining health and functioning of the holobiont. However, the coral holobiont contains both dead and living bacteria. The former can be the result of corals feeding on bacteria, rapid swings from hyper- to hypoxic conditions in the coral tissue, the presence of antimicrobial compounds in coral mucus, and an abundance of lytic bacteriophages. By combining propidium monoazide (PMA) treatment with high-throughput sequencing on six coral species (Acropora loripes, A. millepora, A. kenti, Platygyra daedalea, Pocillopora acuta, and Porites lutea) we were able to obtain information on bacterial communities with little noise from non-viable microbial DNA. Metabarcoding of the 16S rRNA gene showed significantly higher community evenness (85%) and species diversity (31%) in untreated compared with PMA-treated tissue for A. loripes only. While PMA-treated coral did not differ significantly from untreated samples in terms of observed number of ASVs, > 30% of ASVs were identified in untreated samples only, suggesting that they originated from cell-free/non-viable DNA. Further, the bacterial community structure was significantly different between PMA-treated and untreated samples for A. loripes and P. acuta indicating that DNA from non-viable microbes can bias community composition data in coral species with low bacterial diversity. Our study is highly relevant to microbiome studies on coral and other host organisms as it delivers a solution to excluding non-viable DNA in a complex community. These results provide novel insights into the dynamic nature of host-associated microbiomes and underline the importance of applying versatile tools in the analysis of metabarcoding or next-generation sequencing data sets.","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"16 1","pages":""},"PeriodicalIF":7.9,"publicationDate":"2023-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138553197","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Repeated exposure of wheat to the fungal root pathogen Bipolaris sorokiniana modulates rhizosphere microbiome assembly and disease suppressiveness. 小麦重复暴露于真菌根部病原体 Bipolaris sorokiniana 会调节根瘤微生物组的组合和病害抑制能力。
IF 7.9 2区 环境科学与生态学 Q1 GENETICS & HEREDITY Pub Date : 2023-12-05 DOI: 10.1186/s40793-023-00529-2
Lilian S Abreu Soares Costa, Mírian Rabelo de Faria, Josiane Barros Chiaramonte, Lucas W Mendes, Edis Sepo, Mattias de Hollander, José Maurício Cunha Fernandes, Víctor J Carrión, Wagner Bettiol, Tim H Mauchline, Jos M Raaijmakers, Rodrigo Mendes

Background: Disease suppressiveness of soils to fungal root pathogens is typically induced in the field by repeated infections of the host plant and concomitant changes in the taxonomic composition and functional traits of the rhizosphere microbiome. Here, we studied this remarkable phenomenon for Bipolaris sorokiniana in two wheat cultivars differing in resistance to this fungal root pathogen.

Results: The results showed that repeated exposure of the susceptible wheat cultivar to the pathogen led to a significant reduction in disease severity after five successive growth cycles. Surprisingly, the resistant wheat cultivar, initially included as a control, showed the opposite pattern with an increase in disease severity after repeated pathogen exposure. Amplicon analyses revealed that the bacterial families Chitinophagaceae, Anaerolineaceae and Nitrosomonadaceae were associated with disease suppressiveness in the susceptible wheat cultivar; disease suppressiveness in the resistant wheat cultivar was also associated with Chitinophagaceae and a higher abundance of Comamonadaceae. Metagenome analysis led to the selection of 604 Biosynthetic Gene Clusters (BGCs), out of a total of 2,571 identified by AntiSMASH analysis, that were overrepresented when the soil entered the disease suppressive state. These BGCs are involved in the biosynthesis of terpenes, non-ribosomal peptides, polyketides, aryl polyenes and post-translationally modified peptides.

Conclusion: Combining taxonomic and functional profiling we identified key changes in the rhizosphere microbiome during disease suppression. This illustrates how the host plant relies on the rhizosphere microbiome as the first line of defense to fight soil-borne pathogens. Microbial taxa and functions identified here can be used in novel strategies to control soil-borne fungal pathogens.

背景:土壤对真菌根部病原体的病害抑制作用通常是通过寄主植物的反复感染以及根瘤微生物组的分类组成和功能特征的相应变化而在田间诱发的。在这里,我们研究了两种小麦栽培品种对 Bipolaris sorokiniana 的这一显著现象,这两种栽培品种对这种真菌根病原体的抗性不同:结果:研究结果表明,易感小麦栽培品种在连续五个生长周期后,病害严重程度显著降低。令人惊讶的是,最初作为对照的抗病小麦栽培品种却表现出相反的模式,在多次接触病原体后病害严重程度增加。扩增子分析表明,细菌科嗜甲壳素科(Chitinophagaceae)、厌氧菌科(Anaerolineaceae)和亚硝基单胞菌科(Nitrosomonadaceae)与易感小麦栽培品种的病害抑制能力有关;抗性小麦栽培品种的病害抑制能力也与嗜甲壳素科(Chitinophagaceae)和较多的拟杆菌科(Comamonadaceae)有关。通过元基因组分析,从 AntiSMASH 分析确定的 2571 个生物合成基因簇(BGC)中筛选出 604 个,这些基因簇在土壤进入抑病状态时具有较高的代表性。这些 BGCs 参与了萜类、非核糖体肽、多酮类、芳基多烯类和翻译后修饰肽的生物合成:结合分类学和功能分析,我们确定了根瘤微生物组在抑制病害过程中的关键变化。这说明了寄主植物是如何依赖根瘤微生物组作为对抗土传病原体的第一道防线的。这里发现的微生物类群和功能可用于控制土传真菌病原体的新策略。
{"title":"Repeated exposure of wheat to the fungal root pathogen Bipolaris sorokiniana modulates rhizosphere microbiome assembly and disease suppressiveness.","authors":"Lilian S Abreu Soares Costa, Mírian Rabelo de Faria, Josiane Barros Chiaramonte, Lucas W Mendes, Edis Sepo, Mattias de Hollander, José Maurício Cunha Fernandes, Víctor J Carrión, Wagner Bettiol, Tim H Mauchline, Jos M Raaijmakers, Rodrigo Mendes","doi":"10.1186/s40793-023-00529-2","DOIUrl":"10.1186/s40793-023-00529-2","url":null,"abstract":"<p><strong>Background: </strong>Disease suppressiveness of soils to fungal root pathogens is typically induced in the field by repeated infections of the host plant and concomitant changes in the taxonomic composition and functional traits of the rhizosphere microbiome. Here, we studied this remarkable phenomenon for Bipolaris sorokiniana in two wheat cultivars differing in resistance to this fungal root pathogen.</p><p><strong>Results: </strong>The results showed that repeated exposure of the susceptible wheat cultivar to the pathogen led to a significant reduction in disease severity after five successive growth cycles. Surprisingly, the resistant wheat cultivar, initially included as a control, showed the opposite pattern with an increase in disease severity after repeated pathogen exposure. Amplicon analyses revealed that the bacterial families Chitinophagaceae, Anaerolineaceae and Nitrosomonadaceae were associated with disease suppressiveness in the susceptible wheat cultivar; disease suppressiveness in the resistant wheat cultivar was also associated with Chitinophagaceae and a higher abundance of Comamonadaceae. Metagenome analysis led to the selection of 604 Biosynthetic Gene Clusters (BGCs), out of a total of 2,571 identified by AntiSMASH analysis, that were overrepresented when the soil entered the disease suppressive state. These BGCs are involved in the biosynthesis of terpenes, non-ribosomal peptides, polyketides, aryl polyenes and post-translationally modified peptides.</p><p><strong>Conclusion: </strong>Combining taxonomic and functional profiling we identified key changes in the rhizosphere microbiome during disease suppression. This illustrates how the host plant relies on the rhizosphere microbiome as the first line of defense to fight soil-borne pathogens. Microbial taxa and functions identified here can be used in novel strategies to control soil-borne fungal pathogens.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"18 1","pages":"85"},"PeriodicalIF":7.9,"publicationDate":"2023-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10696838/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138488799","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","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 coral-associated actinobacterium mitigates coral bleaching under heat stress. 一种与珊瑚有关的放线菌减轻了高温下珊瑚的白化。
IF 7.9 2区 环境科学与生态学 Q1 GENETICS & HEREDITY Pub Date : 2023-11-23 DOI: 10.1186/s40793-023-00540-7
Jie Li, Yiyang Zou, Qiqi Li, Jian Zhang, David G Bourne, Yuanjiao Lyu, Cong Liu, Si Zhang

Background: The positive effects of exposing corals to microorganisms have been reported though how the benefits are conferred are poorly understood. Here, we isolated an actinobacterial strain (SCSIO 13291) from Pocillopora damicornis with capabilities to synthesize antioxidants, vitamins, and antibacterial and antiviral compounds supported with phenotypic and/or genomic evidence. Strain SCSIO 13291 was labeled with 5 (and - 6)-carboxytetramethylrhodamine, succinimidyl ester and the labeled cell suspension directly inoculated onto the coral polyp tissues when nubbins were under thermal stress in a mesocosm experiment. We then visualized the labelled bacterial cells and analyzed the coral physiological, transcriptome and microbiome to elucidate the effect this strain conferred on the coral holobiont under thermal stress.

Results: Subsequent microscopic observations confirmed the presence of the bacterium attached to the coral polyps. Addition of the SCSIO 13291 strain reduced signs of bleaching in the corals subjected to heat stress. At the same time, alterations in gene expression, which were involved in reactive oxygen species and light damage mitigation, attenuated apoptosis and exocytosis in addition to metabolite utilization, were observed in the coral host and Symbiodiniaceae populations. In addition, the coral associated bacterial community altered with a more stable ecological network for samples inoculated with the bacterial strain.

Conclusions: Our results provide insights into the benefits of a putative actinobacterial probiotic strain that mitigate coral bleaching signs. This study suggests that the inoculation of bacteria can potentially directly benefit the coral holobiont through conferring metabolic activities or through indirect mechanisms of suppling additional nutrient sources.

背景:已经报道了珊瑚暴露于微生物的积极影响,但人们对这些好处是如何产生的却知之甚少。在这里,我们从达米角Pocillopora damicornis中分离出一株放线菌菌株(SCSIO 13291),该菌株具有合成抗氧化剂、维生素、抗菌和抗病毒化合物的能力,并得到表型和/或基因组证据的支持。用5(和- 6)-羧基四甲基罗丹明、琥珀酰亚胺酯对菌株SCSIO 13291进行标记,并将标记的细胞悬浮液直接接种到珊瑚虫组织中,进行热应激实验。然后,我们将标记的细菌细胞可视化,并分析珊瑚的生理,转录组和微生物组,以阐明该菌株在热应激下对珊瑚全息生物的影响。结果:随后的显微镜观察证实了附着在珊瑚虫上的细菌的存在。添加SCSIO 13291菌株减少了受热应力影响的珊瑚的白化迹象。与此同时,在珊瑚宿主和共生体科种群中观察到基因表达的变化,这些变化涉及活性氧和光损伤缓解、细胞凋亡减弱和胞吐以及代谢物利用。此外,与珊瑚相关的细菌群落在接种菌株的样品中发生了更稳定的生态网络变化。结论:我们的研究结果提供了一种假定的放线菌益生菌菌株减轻珊瑚白化迹象的好处。这项研究表明,接种细菌可以通过赋予代谢活动或通过提供额外营养来源的间接机制,潜在地直接使珊瑚全息生物受益。
{"title":"A coral-associated actinobacterium mitigates coral bleaching under heat stress.","authors":"Jie Li, Yiyang Zou, Qiqi Li, Jian Zhang, David G Bourne, Yuanjiao Lyu, Cong Liu, Si Zhang","doi":"10.1186/s40793-023-00540-7","DOIUrl":"10.1186/s40793-023-00540-7","url":null,"abstract":"<p><strong>Background: </strong>The positive effects of exposing corals to microorganisms have been reported though how the benefits are conferred are poorly understood. Here, we isolated an actinobacterial strain (SCSIO 13291) from Pocillopora damicornis with capabilities to synthesize antioxidants, vitamins, and antibacterial and antiviral compounds supported with phenotypic and/or genomic evidence. Strain SCSIO 13291 was labeled with 5 (and - 6)-carboxytetramethylrhodamine, succinimidyl ester and the labeled cell suspension directly inoculated onto the coral polyp tissues when nubbins were under thermal stress in a mesocosm experiment. We then visualized the labelled bacterial cells and analyzed the coral physiological, transcriptome and microbiome to elucidate the effect this strain conferred on the coral holobiont under thermal stress.</p><p><strong>Results: </strong>Subsequent microscopic observations confirmed the presence of the bacterium attached to the coral polyps. Addition of the SCSIO 13291 strain reduced signs of bleaching in the corals subjected to heat stress. At the same time, alterations in gene expression, which were involved in reactive oxygen species and light damage mitigation, attenuated apoptosis and exocytosis in addition to metabolite utilization, were observed in the coral host and Symbiodiniaceae populations. In addition, the coral associated bacterial community altered with a more stable ecological network for samples inoculated with the bacterial strain.</p><p><strong>Conclusions: </strong>Our results provide insights into the benefits of a putative actinobacterial probiotic strain that mitigate coral bleaching signs. This study suggests that the inoculation of bacteria can potentially directly benefit the coral holobiont through conferring metabolic activities or through indirect mechanisms of suppling additional nutrient sources.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"18 1","pages":"83"},"PeriodicalIF":7.9,"publicationDate":"2023-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10668361/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138300369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Grapevine bacterial communities display compartment-specific dynamics over space and time within the Central Valley of California. 葡萄藤细菌群落在加利福尼亚中央山谷的空间和时间上显示出特定的动态。
IF 7.9 2区 环境科学与生态学 Q1 GENETICS & HEREDITY Pub Date : 2023-11-23 DOI: 10.1186/s40793-023-00539-0
Joel F Swift, Zoë Migicovsky, Grace E Trello, Allison J Miller

Background: Plant organs (compartments) host distinct microbiota which shift in response to variation in both development and climate. Grapevines are woody perennial crops that are clonally propagated and cultivated across vast geographic areas, and as such, their microbial communities may also reflect site-specific influences. These site-specific influences along with microbial differences across sites compose 'terroir', the environmental influence on wine produced in a given region. Commercial grapevines are typically composed of a genetically distinct root (rootstock) grafted to a shoot system (scion) which adds an additional layer of complexity via genome-to-genome interactions.

Results: To understand spatial and temporal patterns of bacterial diversity in grafted grapevines, we used 16S rRNA amplicon sequencing to quantify soil and compartment microbiota (berries, leaves, and roots) for grafted grapevines in commercial vineyards across three counties in the Central Valley of California over two successive growing seasons. Community composition revealed compartment-specific dynamics. Roots assembled site-specific bacterial communities that reflected rootstock genotype and environment influences, whereas bacterial communities of leaves and berries displayed associations with time.

Conclusions: These results provide further evidence of a microbial terroir within the grapevine root systems but also reveal that the microbiota of above-ground compartments are only weakly associated with the local soil microbiome in the Central Valley of California.

背景:植物器官(室室)寄主不同的微生物群,这些微生物群随着发育和气候的变化而变化。葡萄藤是一种多年生木本作物,在广阔的地理区域进行无性繁殖和栽培,因此,它们的微生物群落也可能反映出特定地点的影响。这些特定地点的影响以及不同地点之间的微生物差异构成了“风土”,即环境对特定地区生产的葡萄酒的影响。商品葡萄藤通常由遗传上不同的根(砧木)嫁接到茎系统(接穗)上,通过基因组与基因组的相互作用增加了额外的复杂性。结果:为了了解嫁接葡萄藤中细菌多样性的时空格局,我们使用16S rRNA扩增子测序技术,在连续两个生长季节对加州中央山谷三个县的商业葡萄园嫁接葡萄藤的土壤和隔室微生物群(浆果、叶子和根)进行了量化。群落组成揭示了区室特有的动态。根系聚集的特定位点细菌群落反映了砧木基因型和环境的影响,而叶片和浆果的细菌群落则与时间有关。结论:这些结果为葡萄藤根系内的微生物风土提供了进一步的证据,但也揭示了在加利福尼亚中央山谷,地上隔室的微生物群与当地土壤微生物群的关系很弱。
{"title":"Grapevine bacterial communities display compartment-specific dynamics over space and time within the Central Valley of California.","authors":"Joel F Swift, Zoë Migicovsky, Grace E Trello, Allison J Miller","doi":"10.1186/s40793-023-00539-0","DOIUrl":"10.1186/s40793-023-00539-0","url":null,"abstract":"<p><strong>Background: </strong>Plant organs (compartments) host distinct microbiota which shift in response to variation in both development and climate. Grapevines are woody perennial crops that are clonally propagated and cultivated across vast geographic areas, and as such, their microbial communities may also reflect site-specific influences. These site-specific influences along with microbial differences across sites compose 'terroir', the environmental influence on wine produced in a given region. Commercial grapevines are typically composed of a genetically distinct root (rootstock) grafted to a shoot system (scion) which adds an additional layer of complexity via genome-to-genome interactions.</p><p><strong>Results: </strong>To understand spatial and temporal patterns of bacterial diversity in grafted grapevines, we used 16S rRNA amplicon sequencing to quantify soil and compartment microbiota (berries, leaves, and roots) for grafted grapevines in commercial vineyards across three counties in the Central Valley of California over two successive growing seasons. Community composition revealed compartment-specific dynamics. Roots assembled site-specific bacterial communities that reflected rootstock genotype and environment influences, whereas bacterial communities of leaves and berries displayed associations with time.</p><p><strong>Conclusions: </strong>These results provide further evidence of a microbial terroir within the grapevine root systems but also reveal that the microbiota of above-ground compartments are only weakly associated with the local soil microbiome in the Central Valley of California.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"18 1","pages":"84"},"PeriodicalIF":7.9,"publicationDate":"2023-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10668525/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138300370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","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 tapestry of the Shulgan-Tash cave (Southern Ural, Russia): influences of environmental factors on the taxonomic composition of the cave biofilms. 俄罗斯南乌拉尔舒尔干—塔什洞穴微生物毯:环境因素对洞穴生物膜分类组成的影响
IF 7.9 2区 环境科学与生态学 Q1 GENETICS & HEREDITY Pub Date : 2023-11-21 DOI: 10.1186/s40793-023-00538-1
Natalia Gogoleva, Olga Chervyatsova, Alexander Balkin, Lyudmila Kuzmina, Elena Shagimardanova, Daria Kiseleva, Yuri Gogolev

Background: Cave biotopes are characterized by stable low temperatures, high humidity, and scarcity of organic substrates. Despite the harsh oligotrophic conditions, they are often inhabited by rich microbial communities. Abundant fouling with a wide range of morphology and coloration of colonies covers the walls of the Shulgan-Tash cave in the Southern Urals. This cave is also famous for the unique Paleolithic painting discovered in the middle of the last century. We aimed to investigate the diversity, distribution, and potential impact of these biofilms on the cave's Paleolithic paintings, while exploring how environmental factors influence the microbial communities within the cave.

Results: The cave's biofilm morphotypes were categorized into three types based on the ultrastructural similarities. Molecular taxonomic analysis identified two main clusters of microbial communities, with Actinobacteria dominating in most of them and a unique "CaveCurd" community with Gammaproteobacteria prevalent in the deepest cave sections. The species composition of these biofilms reflects changes in environmental conditions, such as substrate composition, temperature, humidity, ventilation, and CO2 content. Additionally, it was observed that cave biofilms contribute to biocorrosion on cave wall surfaces.

Conclusions: The Shulgan-Tash cave presents an intriguing example of a stable extreme ecosystem with diverse microbiota. However, the intense dissolution and deposition of carbonates caused by Actinobacteria pose a potential threat to the preservation of the cave's ancient rock paintings.

背景:洞穴生物群落以稳定的低温、高湿和缺乏有机基质为特征。尽管恶劣的贫营养条件,他们往往居住着丰富的微生物群落。乌拉尔南部舒尔干-塔什洞穴的墙壁上覆盖着丰富的污垢,其形态和颜色各异。这个洞穴也因上世纪中叶发现的独特的旧石器时代绘画而闻名。我们的目的是研究这些生物膜的多样性、分布及其对洞穴旧石器时代壁画的潜在影响,同时探索环境因素如何影响洞穴内的微生物群落。结果:基于超微结构相似性,将洞穴生物膜形态分为三种类型。分子分类分析确定了两个主要的微生物群落群,其中放线菌群占多数,而一个独特的“CaveCurd”群落,其中γ变形菌群普遍存在于最深的洞穴部分。这些生物膜的物种组成反映了环境条件的变化,如基质组成、温度、湿度、通风和CO2含量。此外,还观察到洞穴生物膜对洞穴壁表面的生物腐蚀有促进作用。结论:舒尔干-塔什洞穴提供了一个具有多种微生物群的稳定极端生态系统的有趣例子。然而,放线菌引起的碳酸盐的强烈溶解和沉积对洞穴古代岩画的保存构成了潜在的威胁。
{"title":"Microbial tapestry of the Shulgan-Tash cave (Southern Ural, Russia): influences of environmental factors on the taxonomic composition of the cave biofilms.","authors":"Natalia Gogoleva, Olga Chervyatsova, Alexander Balkin, Lyudmila Kuzmina, Elena Shagimardanova, Daria Kiseleva, Yuri Gogolev","doi":"10.1186/s40793-023-00538-1","DOIUrl":"10.1186/s40793-023-00538-1","url":null,"abstract":"<p><strong>Background: </strong>Cave biotopes are characterized by stable low temperatures, high humidity, and scarcity of organic substrates. Despite the harsh oligotrophic conditions, they are often inhabited by rich microbial communities. Abundant fouling with a wide range of morphology and coloration of colonies covers the walls of the Shulgan-Tash cave in the Southern Urals. This cave is also famous for the unique Paleolithic painting discovered in the middle of the last century. We aimed to investigate the diversity, distribution, and potential impact of these biofilms on the cave's Paleolithic paintings, while exploring how environmental factors influence the microbial communities within the cave.</p><p><strong>Results: </strong>The cave's biofilm morphotypes were categorized into three types based on the ultrastructural similarities. Molecular taxonomic analysis identified two main clusters of microbial communities, with Actinobacteria dominating in most of them and a unique \"CaveCurd\" community with Gammaproteobacteria prevalent in the deepest cave sections. The species composition of these biofilms reflects changes in environmental conditions, such as substrate composition, temperature, humidity, ventilation, and CO<sub>2</sub> content. Additionally, it was observed that cave biofilms contribute to biocorrosion on cave wall surfaces.</p><p><strong>Conclusions: </strong>The Shulgan-Tash cave presents an intriguing example of a stable extreme ecosystem with diverse microbiota. However, the intense dissolution and deposition of carbonates caused by Actinobacteria pose a potential threat to the preservation of the cave's ancient rock paintings.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":"18 1","pages":"82"},"PeriodicalIF":7.9,"publicationDate":"2023-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10662634/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138292111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
期刊
Environmental Microbiome
全部 Acc. Chem. Res. ACS Applied Bio Materials ACS Appl. Electron. Mater. ACS Appl. Energy Mater. ACS Appl. Mater. Interfaces ACS Appl. Nano Mater. ACS Appl. Polym. Mater. ACS BIOMATER-SCI ENG ACS Catal. ACS Cent. Sci. ACS Chem. Biol. ACS Chemical Health & Safety ACS Chem. Neurosci. ACS Comb. Sci. ACS Earth Space Chem. ACS Energy Lett. ACS Infect. Dis. ACS Macro Lett. ACS Mater. Lett. ACS Med. Chem. Lett. ACS Nano ACS Omega ACS Photonics ACS Sens. ACS Sustainable Chem. Eng. ACS Synth. Biol. Anal. Chem. BIOCHEMISTRY-US Bioconjugate Chem. BIOMACROMOLECULES Chem. Res. Toxicol. Chem. Rev. Chem. Mater. CRYST GROWTH DES ENERG FUEL Environ. Sci. Technol. Environ. Sci. Technol. Lett. Eur. J. Inorg. Chem. IND ENG CHEM RES Inorg. Chem. J. Agric. Food. Chem. J. Chem. Eng. Data J. Chem. Educ. J. Chem. Inf. Model. J. Chem. Theory Comput. J. Med. Chem. J. Nat. Prod. J PROTEOME RES J. Am. Chem. Soc. LANGMUIR MACROMOLECULES Mol. Pharmaceutics Nano Lett. Org. Lett. ORG PROCESS RES DEV ORGANOMETALLICS J. Org. Chem. J. Phys. Chem. J. Phys. Chem. A J. Phys. Chem. B J. Phys. Chem. C J. Phys. Chem. Lett. Analyst Anal. Methods Biomater. Sci. Catal. Sci. Technol. Chem. Commun. Chem. Soc. Rev. CHEM EDUC RES PRACT CRYSTENGCOMM Dalton Trans. Energy Environ. Sci. ENVIRON SCI-NANO ENVIRON SCI-PROC IMP ENVIRON SCI-WAT RES Faraday Discuss. Food Funct. Green Chem. Inorg. Chem. Front. Integr. Biol. J. Anal. At. Spectrom. J. Mater. Chem. A J. Mater. Chem. B J. Mater. Chem. C Lab Chip Mater. Chem. Front. Mater. Horiz. MEDCHEMCOMM Metallomics Mol. Biosyst. Mol. Syst. Des. Eng. Nanoscale Nanoscale Horiz. Nat. Prod. Rep. New J. Chem. Org. Biomol. Chem. Org. Chem. Front. PHOTOCH PHOTOBIO SCI PCCP Polym. Chem.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1