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Exploring freshwater stream bacterial communities as indicators of land use intensity. 探索作为土地利用强度指标的淡水溪流细菌群落。
IF 6.2 2区 环境科学与生态学 Q1 GENETICS & HEREDITY Pub Date : 2024-07-08 DOI: 10.1186/s40793-024-00588-z
Syrie Hermans, Anju Gautam, Gillian D Lewis, Martin Neale, Hannah L Buckley, Bradley S Case, Gavin Lear

Background: Stream ecosystems comprise complex interactions among biological communities and their physicochemical surroundings, contributing to their overall ecological health. Despite this, many monitoring programs ignore changes in the bacterial communities that are the base of food webs in streams, often focusing on stream physicochemical assessments or macroinvertebrate community diversity instead. We used 16S rRNA gene sequencing to assess bacterial community compositions within 600 New Zealand stream biofilm samples from 204 sites within a 6-week period (February-March 2010). Sites were either dominated by indigenous forests, exotic plantation forests, horticulture, or pastoral grasslands in the upstream catchment. We sought to predict each site's catchment land use and environmental conditions based on the composition of the stream bacterial communities.

Results: Random forest modelling allowed us to use bacterial community composition to predict upstream catchment land use with 65% accuracy; urban sites were correctly assigned 90% of the time. Despite the variation inherent when sampling across a ~ 1000-km distance, bacterial community data could correctly differentiate undisturbed sites, grouped by their dominant environmental properties, with 75% accuracy. The positive correlations between actual values and those predicted by the models built using the stream biofilm bacterial data ranged from weak (average log N concentration in the stream water, R2 = 0.02) to strong (annual mean air temperature, R2 = 0.69).

Conclusions: Freshwater bacterial community data provide useful insights into land use impacts on stream ecosystems; they may be used as an additional measure to screen stream catchment attributes.

背景:溪流生态系统由生物群落与其周围的物理化学环境之间复杂的相互作用组成,对其整体生态健康起着重要作用。尽管如此,许多监测项目却忽视了作为溪流食物网基础的细菌群落的变化,而往往侧重于溪流理化评估或大型无脊椎动物群落多样性。我们利用 16S rRNA 基因测序技术评估了新西兰溪流生物膜样本中的细菌群落组成,这些样本来自 204 个地点,时间跨度为 6 周(2010 年 2 月至 3 月)。这些地点的上游集水区以本土森林、外来人工林、园艺或牧草地为主。我们试图根据溪流细菌群落的组成来预测每个地点的集水区土地利用和环境条件:随机森林模型使我们能够利用细菌群落组成预测上游集水区的土地利用情况,准确率为 65%;90% 的情况下,城市站点被正确分配。尽管在约 1000 千米的距离内取样会产生固有的差异,但细菌群落数据可以正确区分未受干扰的地点(按其主要环境属性分组),准确率为 75%。实际值与利用溪流生物膜细菌数据建立的模型预测值之间的正相关性从弱(溪流水中平均对数 N 浓度,R2 = 0.02)到强(年平均气温,R2 = 0.69)不等:淡水细菌群落数据为了解土地利用对溪流生态系统的影响提供了有用的信息;可将其作为筛选溪流集水属性的额外措施。
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引用次数: 0
Survival strategies of aerobic methanotrophs under hypoxia in methanogenic lake sediments. 产甲烷湖泊沉积物中缺氧条件下需氧养甲烷生物的生存策略。
IF 6.2 2区 环境科学与生态学 Q1 GENETICS & HEREDITY Pub Date : 2024-07-02 DOI: 10.1186/s40793-024-00586-1
Almog Gafni, Maxim Rubin-Blum, Colin Murrell, Hanni Vigderovich, Werner Eckert, Nasmille Larke-Mejía, Orit Sivan
<p><strong>Background: </strong>Microbial methane oxidation, methanotrophy, plays a crucial role in mitigating the release of the potent greenhouse gas methane from aquatic systems. While aerobic methanotrophy is a well-established process in oxygen-rich environments, emerging evidence suggests their activity in hypoxic conditions. However, the adaptability of these methanotrophs to such environments has remained poorly understood. Here, we explored the genetic adaptability of aerobic methanotrophs to hypoxia in the methanogenic sediments of Lake Kinneret (LK). These LK methanogenic sediments, situated below the oxidic and sulfidic zones, were previously characterized by methane oxidation coupled with iron reduction via the involvement of aerobic methanotrophs.</p><p><strong>Results: </strong>In order to explore the adaptation of the methanotrophs to hypoxia, we conducted two experiments using LK sediments as inoculum: (i) an aerobic "classical" methanotrophic enrichment with ambient air employing DNA stable isotope probing (DNA-SIP) and (ii) hypoxic methanotrophic enrichment with repeated spiking of 1% oxygen. Analysis of 16S rRNA gene amplicons revealed the enrichment of Methylococcales methanotrophs, being up to a third of the enriched community. Methylobacter, Methylogaea, and Methylomonas were prominent in the aerobic experiment, while hypoxic conditions enriched primarily Methylomonas. Using metagenomics sequencing of DNA extracted from these experiments, we curated five Methylococcales metagenome-assembled genomes (MAGs) and evaluated the genetic basis for their survival in hypoxic environments. A comparative analysis with an additional 62 Methylococcales genomes from various environments highlighted several core genetic adaptations to hypoxia found in most examined Methylococcales genomes, including high-affinity cytochrome oxidases, oxygen-binding proteins, fermentation-based methane oxidation, motility, and glycogen use. We also found that some Methylococcales, including LK Methylococcales, may denitrify, while metals and humic substances may also serve as electron acceptors alternative to oxygen. Outer membrane multi-heme cytochromes and riboflavin were identified as potential mediators for the utilization of metals and humic material. These diverse mechanisms suggest the ability of methanotrophs to thrive in ecological niches previously thought inhospitable for their growth.</p><p><strong>Conclusions: </strong>Our study sheds light on the ability of enriched Methylococcales methanotrophs from methanogenic LK sediments to survive under hypoxia. Genomic analysis revealed a spectrum of genetic capabilities, potentially enabling these methanotrophs to function. The identified mechanisms, such as those enabling the use of alternative electron acceptors, expand our understanding of methanotroph resilience in diverse ecological settings. These findings contribute to the broader knowledge of microbial methane oxidation and have implications f
背景:微生物甲烷氧化(即甲烷营养作用)在减少水生系统释放强效温室气体甲烷方面发挥着至关重要的作用。虽然好氧甲烷营养体在富氧环境中是一个成熟的过程,但新出现的证据表明它们在缺氧条件下也有活动。然而,人们对这些甲烷营养体对这种环境的适应性仍然知之甚少。在这里,我们探讨了好氧甲烷营养体在基纳特湖(LK)产甲烷沉积物中对缺氧的遗传适应性。这些位于氧化带和硫化带之下的湖泊甲烷沉积物以前的特点是甲烷氧化与好氧甲烷营养体参与的铁还原作用:为了探索甲烷营养体对缺氧的适应性,我们使用 LK 沉积物作为接种体进行了两项实验:(i) 利用 DNA 稳定同位素探针(DNA-SIP)对环境空气进行好氧 "经典 "甲烷营养体富集;(ii) 反复添加 1% 氧气进行缺氧甲烷营养体富集。对 16S rRNA 基因扩增子的分析表明,富集了甲基球菌属甲烷营养群落,占富集群落的三分之一。在有氧实验中,甲基芽孢杆菌(Methylobacter)、甲基芽孢杆菌(Methylogaea)和甲基单胞菌(Methylomonas)最为突出,而在缺氧条件下,主要富集的是甲基单胞菌。通过对从这些实验中提取的 DNA 进行元基因组学测序,我们整理出了五个甲基球菌元基因组组装基因组(MAGs),并评估了它们在缺氧环境中生存的遗传基础。通过与另外 62 个来自不同环境的甲球藻基因组进行比较分析,我们发现在大多数被研究的甲球藻基因组中都存在几种适应缺氧环境的核心基因,包括高亲和性细胞色素氧化酶、氧结合蛋白、基于发酵的甲烷氧化、运动性和糖原利用。我们还发现,包括 LK 甲基球菌在内的一些甲基球菌可进行反硝化,而金属和腐殖质也可作为氧气以外的电子受体。外膜多血红素细胞色素和核黄素被认为是利用金属和腐殖质的潜在媒介。这些不同的机制表明,甲烷营养体有能力在以前认为不适合其生长的生态位中茁壮成长:我们的研究揭示了产甲烷 LK 沉积物中富集的甲基球菌甲烷营养体在缺氧条件下的生存能力。基因组分析揭示了一系列遗传能力,这些能力可能使这些甲烷营养体发挥作用。所发现的机制,如使用替代电子受体的机制,拓展了我们对甲烷营养体在不同生态环境中的恢复能力的认识。这些发现有助于拓宽微生物甲烷氧化的知识面,并对理解甲烷营养体在各种环境条件下减少甲烷排放的潜在贡献具有影响。
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引用次数: 0
Metagenomic insights into Heimdallarchaeia clades from the deep-sea cold seep and hydrothermal vent. 深海冷渗漏和热液喷口 Heimdallarchaeia 支系的元基因组研究。
IF 6.2 2区 环境科学与生态学 Q2 Immunology and Microbiology Pub Date : 2024-06-22 DOI: 10.1186/s40793-024-00585-2
Rui Liu, Ruining Cai, Minxiao Wang, Jing Zhang, Huan Zhang, Chaolun Li, Chaomin Sun

Heimdallarchaeia is a class of the Asgardarchaeota, are the most probable candidates for the archaeal protoeukaryote ancestor that have been identified to date. However, little is known about their life habits regardless of their ubiquitous distribution in diverse habitats, which is especially true for Heimdallarchaeia from deep-sea environments. In this study, we obtained 13 metagenome-assembled genomes (MAGs) of Heimdallarchaeia from the deep-sea cold seep and hydrothermal vent. These MAGs belonged to orders o_Heimdallarchaeales and o_JABLTI01, and most of them (9 MAGs) come from the family f_Heimdallarchaeaceae according to genome taxonomy database (GTDB). These are enriched for common eukaryote-specific signatures. Our results show that these Heimdallarchaeia have the metabolic potential to reduce sulfate (assimilatory) and nitrate (dissimilatory) to sulfide and ammonia, respectively, suggesting a previously unappreciated role in biogeochemical cycling. Furthermore, we find that they could perform both TCA and rTCA pathways coupled with pyruvate metabolism for energy conservation, fix CO2 and generate organic compounds through an atypical Wood-Ljungdahl pathway. In addition, many genes closely associated with bacteriochlorophyll and carotenoid biosynthesis, and oxygen-dependent metabolic pathways are identified in these Heimdallarchaeia MAGs, suggesting a potential light-utilization by pigments and microoxic lifestyle. Taken together, our results indicate that Heimdallarchaeia possess a mixotrophic lifestyle, which may give them more flexibility to adapt to the harsh deep-sea conditions.

海姆达尔古菌(Heimdallarchaeia)是阿斯加德古菌群(Asgardarchaeota)中的一类,是迄今为止已确定的古原核生物祖先的最可能候选者。然而,人们对它们的生活习性知之甚少,尽管它们无处不在地分布于不同的栖息地,尤其是深海环境中的海姆达尔古菌(Heimdallarchaeia)。在这项研究中,我们从深海冷渗漏和热液喷口获得了 13 个 Heimdallarchaeia 的元基因组组装基因组(MAGs)。根据基因组分类数据库(GTDB),这些MAGs属于o_Heimdallarchaeales和o_JABLTI01目,其中大部分(9个MAGs)来自f_Heimdallarchaeaceae科。这些MAG富含常见的真核生物特异性特征。我们的研究结果表明,这些 Heimdallarchaeia 具有将硫酸盐(同化作用)和硝酸盐(异化作用)分别还原成硫化物和氨的代谢潜能,这表明它们在生物地球化学循环中发挥着以前未被重视的作用。此外,我们还发现它们可以同时进行 TCA 和 rTCA 途径以及丙酮酸代谢以保存能量,并通过非典型伍德-荣格达尔途径固定二氧化碳和生成有机化合物。此外,在这些海姆达尔弓形虫 MAGs 中还发现了许多与细菌叶绿素和类胡萝卜素生物合成密切相关的基因,以及依赖氧的代谢途径,这表明色素和微氧生活方式可能利用光。总之,我们的研究结果表明,海姆达尔弓形虫具有混养的生活方式,这可能使它们更灵活地适应恶劣的深海条件。
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引用次数: 0
Genome streamlining in Parcubacteria transitioning from soil to groundwater. 从土壤过渡到地下水的 Parcubacteria 的基因组精简。
IF 6.2 2区 环境科学与生态学 Q2 Immunology and Microbiology Pub Date : 2024-06-20 DOI: 10.1186/s40793-024-00581-6
Narendrakumar M Chaudhari, Olga M Pérez-Carrascal, Will A Overholt, Kai U Totsche, Kirsten Küsel

Background: To better understand the influence of habitat on the genetic content of bacteria, with a focus on members of Candidate Phyla Radiation (CPR) bacteria, we studied the effects of transitioning from soil via seepage waters to groundwater on genomic composition of ultra-small Parcubacteria, the dominating CPR class in seepage waters, using genome resolved metagenomics.

Results: Bacterial metagenome-assembled genomes (MAGs), (318 total, 32 of Parcubacteria) were generated from seepage waters and compared directly to groundwater counterparts. The estimated average genome sizes of members of major phyla Proteobacteria, Bacteroidota and Cand. Patescibacteria (Candidate Phyla Radiation - CPR bacteria) were significantly higher in soil-seepage water as compared to their groundwater counterparts. Seepage water Parcubacteria (Paceibacteria) exhibited 1.18-fold greater mean genome size and 2-fold lower mean proportion of pseudogenes than those in groundwater. Bacteroidota and Proteobacteria also showed a similar trend of reduced genomes in groundwater compared to seepage. While exploring gene loss and adaptive gains in closely related CPR lineages in groundwater, we identified a membrane protein, and a lipoglycopeptide resistance gene unique to a seepage Parcubacterium genome. A nitrite reductase gene was also identified and was unique to the groundwater Parcubacteria genomes, likely acquired from other planktonic microbes via horizontal gene transfer.

Conclusions: Overall, our data suggest that bacteria in seepage waters, including ultra-small Parcubacteria, have significantly larger genomes and higher metabolic enrichment than their groundwater counterparts, highlighting possible genome streamlining of the latter in response to habitat selection in an oligotrophic environment.

背景:为了更好地了解栖息地对细菌遗传内容的影响,重点是候选菌门辐射(CPR)细菌成员,我们利用基因组解析元基因组学研究了从土壤经渗漏水过渡到地下水对超小型 Parcubacteria(渗漏水中的主要 CPR 类)基因组组成的影响:从渗漏水中生成了细菌元基因组组装基因组(MAGs)(共 318 个,其中 32 个为 Parcubacteria),并直接与地下水中的对应基因组进行了比较。据估计,主要门类蛋白细菌、类杆菌和棒状杆菌(Cand.与地下水相比,土壤渗漏水中的主要门类蛋白质细菌、类细菌和棒状杆菌(辐射候选门类--CPR 细菌)的估计平均基因组大小要高得多。渗漏水中的副杆菌(Paceibacteria)的平均基因组大小比地下水中的副杆菌大 1.18 倍,假基因的平均比例比地下水中的副杆菌低 2 倍。与地下水相比,类细菌和蛋白细菌的基因组也呈现出类似的减少趋势。在探索地下水中密切相关的 CPR 族系的基因缺失和适应性增益时,我们发现了一种膜蛋白和一种脂甘肽抗性基因,这是渗水副杆菌基因组所独有的。我们还发现了一个亚硝酸盐还原酶基因,它是地下水副杆菌基因组所独有的,很可能是通过水平基因转移从其他浮游微生物那里获得的:总之,我们的数据表明,渗漏水中的细菌(包括超小型副杆菌)的基因组比地下水中的细菌大得多,代谢富集度也更高,这表明地下水中的细菌可能是为了适应寡营养环境中的生境选择而精简了基因组。
{"title":"Genome streamlining in Parcubacteria transitioning from soil to groundwater.","authors":"Narendrakumar M Chaudhari, Olga M Pérez-Carrascal, Will A Overholt, Kai U Totsche, Kirsten Küsel","doi":"10.1186/s40793-024-00581-6","DOIUrl":"10.1186/s40793-024-00581-6","url":null,"abstract":"<p><strong>Background: </strong>To better understand the influence of habitat on the genetic content of bacteria, with a focus on members of Candidate Phyla Radiation (CPR) bacteria, we studied the effects of transitioning from soil via seepage waters to groundwater on genomic composition of ultra-small Parcubacteria, the dominating CPR class in seepage waters, using genome resolved metagenomics.</p><p><strong>Results: </strong>Bacterial metagenome-assembled genomes (MAGs), (318 total, 32 of Parcubacteria) were generated from seepage waters and compared directly to groundwater counterparts. The estimated average genome sizes of members of major phyla Proteobacteria, Bacteroidota and Cand. Patescibacteria (Candidate Phyla Radiation - CPR bacteria) were significantly higher in soil-seepage water as compared to their groundwater counterparts. Seepage water Parcubacteria (Paceibacteria) exhibited 1.18-fold greater mean genome size and 2-fold lower mean proportion of pseudogenes than those in groundwater. Bacteroidota and Proteobacteria also showed a similar trend of reduced genomes in groundwater compared to seepage. While exploring gene loss and adaptive gains in closely related CPR lineages in groundwater, we identified a membrane protein, and a lipoglycopeptide resistance gene unique to a seepage Parcubacterium genome. A nitrite reductase gene was also identified and was unique to the groundwater Parcubacteria genomes, likely acquired from other planktonic microbes via horizontal gene transfer.</p><p><strong>Conclusions: </strong>Overall, our data suggest that bacteria in seepage waters, including ultra-small Parcubacteria, have significantly larger genomes and higher metabolic enrichment than their groundwater counterparts, highlighting possible genome streamlining of the latter in response to habitat selection in an oligotrophic environment.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":6.2,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11188291/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141433142","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
Effect of plant communities on bacterial and fungal communities in a Central European grassland. 植物群落对中欧草地细菌和真菌群落的影响。
IF 6.2 2区 环境科学与生态学 Q1 GENETICS & HEREDITY Pub Date : 2024-06-20 DOI: 10.1186/s40793-024-00583-4
Clémentine Lepinay, Tomáš Větrovský, Milan Chytrý, Pavel Dřevojan, Karel Fajmon, Tomáš Cajthaml, Petr Kohout, Petr Baldrian

Background: Grasslands provide fundamental ecosystem services that are supported by their plant diversity. However, the importance of plant taxonomic diversity for the diversity of other taxa in grasslands remains poorly understood. Here, we studied the associations between plant communities, soil chemistry and soil microbiome in a wooded meadow of Čertoryje (White Carpathians, Czech Republic), a European hotspot of plant species diversity.

Results: High plant diversity was associated with treeless grassland areas with high primary productivity and high contents of soil nitrogen and organic carbon. In contrast, low plant diversity occurred in grasslands near solitary trees and forest edges. Fungal communities differed between low-diversity and high-diversity grasslands more strongly than bacterial communities, while the difference in arbuscular mycorrhizal fungi (AMF) depended on their location in soil versus plant roots. Compared to grasslands with low plant diversity, high-diversity plant communities had a higher diversity of fungi including soil AMF, a different fungal and soil AMF community composition and higher bacterial and soil AMF biomass. Root AMF composition differed only slightly between grasslands with low and high plant diversity. Trees dominated the belowground plant community in low-diversity grasslands, which influenced microbial diversity and composition.

Conclusions: The determinants of microbiome abundance and composition in grasslands are complex. Soil chemistry mainly influenced bacterial communities, while plant community type mainly affected fungal (including AMF) communities. Further studies on the functional roles of microbial communities are needed to understand plant-soil-microbe interactions and their involvement in grassland ecosystem services.

背景:草地提供的基本生态系统服务由其植物多样性支持。然而,人们对草地上植物分类多样性对其他类群多样性的重要性仍然知之甚少。在这里,我们研究了欧洲植物物种多样性热点地区 Čertoryje(捷克共和国白喀尔巴阡山脉)有林草甸的植物群落、土壤化学和土壤微生物组之间的关系:结果:植物多样性高与初级生产力高、土壤氮和有机碳含量高的无树草地有关。与此相反,靠近孤树和森林边缘的草地植物多样性较低。真菌群落在低多样性草地和高多样性草地之间的差异比细菌群落更大,而丛枝菌根真菌(AMF)的差异则取决于它们在土壤中的位置和在植物根部的位置。与植物多样性低的草地相比,高多样性植物群落的真菌多样性更高,包括土壤 AMF,真菌和土壤 AMF 群落组成不同,细菌和土壤 AMF 生物量更高。植物多样性低的草地和植物多样性高的草地的根部 AMF 组成仅略有不同。树木在低多样性草地的地下植物群落中占主导地位,这影响了微生物的多样性和组成:结论:决定草地微生物群丰度和组成的因素非常复杂。土壤化学主要影响细菌群落,而植物群落类型主要影响真菌(包括AMF)群落。需要进一步研究微生物群落的功能作用,以了解植物-土壤-微生物之间的相互作用及其在草地生态系统服务中的参与。
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引用次数: 0
Determining the footprint of breeding in the seed microbiome of a perennial cereal. 确定多年生谷物种子微生物组的育种足迹。
IF 7.9 2区 环境科学与生态学 Q2 Immunology and Microbiology Pub Date : 2024-06-17 DOI: 10.1186/s40793-024-00584-3
Kristina Michl, Christophe David, Benjamin Dumont, Linda-Maria Dimitrova Mårtensson, Frank Rasche, Gabriele Berg, Tomislav Cernava

Background: Seed endophytes have a significant impact on plant health and fitness. They can be inherited and passed on to the next plant generation. However, the impact of breeding on their composition in seeds is less understood. Here, we studied the indigenous seed microbiome of a recently domesticated perennial grain crop (Intermediate wheatgrass, Thinopyrum intermedium L.) that promises great potential for harnessing microorganisms to enhance crop performance by a multiphasic approach, including amplicon and strain libraries, as well as molecular and physiological assays.

Results: Intermediate wheatgrass seeds harvested from four field sites in Europe over three consecutive years were dominated by Proteobacteria (88%), followed by Firmicutes (10%). Pantoea was the most abundant genus and Pantoea agglomerans was identified as the only core taxon present in all samples. While bacterial diversity and species richness were similar across all accessions, the relative abundance varied especially in terms of low abundant and rare taxa. Seeds from four different breeding cycles (TLI C3, C5, C704, C801) showed significant differences in bacterial community composition and abundance. We found a decrease in the relative abundance of the functional genes nirK and nifH as well as a drop in bacterial diversity and richness. This was associated with a loss of amplicon sequence variants (ASVs) in Actinobacteria, Alphaproteobacteria, and Bacilli, which could be partially compensated in offspring seeds, which have been cultivated at a new site. Interestingly, only a subset assigned to potentially beneficial bacteria, e.g. Pantoea, Kosakonia, and Pseudomonas, was transmitted to the next plant generation or shared with offspring seeds.

Conclusion: Overall, this study advances our understanding of the assembly and transmission of endophytic seed microorganisms in perennial intermediate wheatgrass and highlights the importance of considering the plant microbiome in future breeding programs.

背景:种子内生菌对植物的健康和适应性有重大影响。它们可以遗传给下一代植物。然而,人们对育种对种子中内生菌组成的影响了解较少。在这里,我们研究了一种最近驯化的多年生谷物作物(中间麦草,Thinopyrum intermedium L.)的本地种子微生物组,通过多相方法,包括扩增子和菌株库以及分子和生理测定,该作物有望利用微生物提高作物性能:连续三年从欧洲四个田间地头收获的中间小麦草种子以变形菌(88%)为主,其次是固着菌(10%)。泛变形菌(Pantoea)是数量最多的菌属,而且泛变形菌聚合体(Pantoea agglomerans)是所有样本中唯一的核心类群。虽然所有样本的细菌多样性和物种丰富度相似,但相对丰富度有所不同,尤其是低丰富度和稀有类群。来自四个不同繁殖周期(TLI C3、C5、C704 和 C801)的种子在细菌群落组成和丰度方面存在显著差异。我们发现功能基因 nirK 和 nifH 的相对丰度有所下降,细菌的多样性和丰富度也有所下降。这与放线菌、副变形菌和芽孢杆菌中扩增序列变体(ASV)的损失有关,但在新地点培育的后代种子中可以得到部分补偿。有趣的是,只有一部分潜在的有益细菌(如泛氏菌、科萨孔菌和假单胞菌)被传递给下一代植物或与后代种子共享:总之,这项研究加深了我们对多年生中间小麦草种子内生微生物的组装和传播的理解,并强调了在未来育种计划中考虑植物微生物组的重要性。
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引用次数: 0
Retraction Note: Metagenome-assembled genomes infer potential microbial metabolism in alkaline sulphidic tailings. 撤稿说明:元基因组组装基因组推断碱性硫化尾矿中潜在的微生物代谢。
IF 7.9 2区 环境科学与生态学 Q2 Immunology and Microbiology Pub Date : 2024-06-12 DOI: 10.1186/s40793-024-00582-5
Wenjun Li, Xiaofang Li
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引用次数: 0
Coral microbiomes are structured by environmental gradients in deep waters. 珊瑚微生物群的结构受深海环境梯度的影响。
IF 7.9 2区 环境科学与生态学 Q2 Immunology and Microbiology Pub Date : 2024-06-10 DOI: 10.1186/s40793-024-00579-0
Samuel A Vohsen, Santiago Herrera

Background: Coral-associated microbiomes vary greatly between colonies and localities with functional consequences on the host. However, the full extent of variability across the ranges of most coral species remains unknown, especially for corals living in deep waters which span greater ranges. Here, we characterized the microbiomes of four octocoral species from mesophotic and bathyal deep-sea habitats in the northern Gulf of Mexico, Muricea pendula, Swiftia exserta, Callogorgia delta, and Paramuricea biscaya, using 16S rRNA gene metabarcoding. We sampled extensively across their ranges to test for microbiome differentiation between and within species, examining the influence of environmental factors that vary with depth (53-2224 m) and geographic location (over 680 m) as well as the host coral's genotype using RAD-sequencing.

Results: Coral microbiomes were often dominated by amplicon sequence variants whose abundances varied across their hosts' ranges, including symbiotic taxa: corallicolids, Endozoicomonas, members of the Mollicutes, and the BD1-7 clade. Coral species, depth, and geographic location significantly affected diversity, microbial community composition, and the relative abundance of individual microbes. Depth was the strongest environmental factor determining microbiome structure within species, which influenced the abundance of most dominant symbiotic taxa. Differences in host genotype, bottom temperature, and surface primary productivity could explain a significant part of the microbiome variation associated with depth and geographic location.

Conclusions: Altogether, this work demonstrates that the microbiomes of corals in deep waters vary substantially across their ranges in accordance with depth and other environmental conditions. It reveals that the influence of depth on the ecology of mesophotic and deep-sea corals extends to its effects on their microbiomes which may have functional consequences. This work also identifies the distributions of microbes including potential parasites which can be used to inform restoration plans in response to the Deepwater Horizon oil spill.

背景:珊瑚相关微生物群在不同的珊瑚群和不同的地方有很大的差异,对宿主的功能产生影响。然而,大多数珊瑚物种在不同范围内的变异程度仍然未知,尤其是生活在深海的珊瑚,它们的分布范围更大。在本文中,我们利用 16S rRNA 基因代谢编码研究了墨西哥湾北部中深海底栖息地和深海底栖息地的四个章珊瑚物种(Muricea pendula、Swiftia exserta、Callogorgia delta 和 Paramuricea biscaya)的微生物组特征。我们在它们的分布范围内进行了广泛采样,以检验微生物组在物种之间和物种内部的差异,并利用 RAD 序列检验了随深度(53-2224 米)和地理位置(680 米以上)变化的环境因素以及宿主珊瑚基因型的影响:结果发现:珊瑚微生物组通常以扩增子序列变体为主,这些变体的丰度在宿主范围内各不相同,其中包括共生类群:珊瑚虫、内生单胞菌、毛霉菌和 BD1-7 支系。珊瑚种类、深度和地理位置对多样性、微生物群落组成和单个微生物的相对丰度有显著影响。深度是决定物种内微生物群落结构的最强环境因素,它影响了大多数优势共生类群的丰度。宿主基因型、底层温度和表层初级生产力的差异可以解释与深度和地理位置相关的微生物群变异的很大一部分原因:总之,这项研究表明,深海珊瑚的微生物组随深度和其他环境条件的不同而在其分布范围内有很大差异。这项研究揭示了深度对中生代珊瑚和深海珊瑚生态学的影响延伸到对其微生物组的影响,这可能会产生功能性后果。这项研究还确定了包括潜在寄生虫在内的微生物的分布,这些微生物可用于为应对深水地平线漏油事件的恢复计划提供信息。
{"title":"Coral microbiomes are structured by environmental gradients in deep waters.","authors":"Samuel A Vohsen, Santiago Herrera","doi":"10.1186/s40793-024-00579-0","DOIUrl":"10.1186/s40793-024-00579-0","url":null,"abstract":"<p><strong>Background: </strong>Coral-associated microbiomes vary greatly between colonies and localities with functional consequences on the host. However, the full extent of variability across the ranges of most coral species remains unknown, especially for corals living in deep waters which span greater ranges. Here, we characterized the microbiomes of four octocoral species from mesophotic and bathyal deep-sea habitats in the northern Gulf of Mexico, Muricea pendula, Swiftia exserta, Callogorgia delta, and Paramuricea biscaya, using 16S rRNA gene metabarcoding. We sampled extensively across their ranges to test for microbiome differentiation between and within species, examining the influence of environmental factors that vary with depth (53-2224 m) and geographic location (over 680 m) as well as the host coral's genotype using RAD-sequencing.</p><p><strong>Results: </strong>Coral microbiomes were often dominated by amplicon sequence variants whose abundances varied across their hosts' ranges, including symbiotic taxa: corallicolids, Endozoicomonas, members of the Mollicutes, and the BD1-7 clade. Coral species, depth, and geographic location significantly affected diversity, microbial community composition, and the relative abundance of individual microbes. Depth was the strongest environmental factor determining microbiome structure within species, which influenced the abundance of most dominant symbiotic taxa. Differences in host genotype, bottom temperature, and surface primary productivity could explain a significant part of the microbiome variation associated with depth and geographic location.</p><p><strong>Conclusions: </strong>Altogether, this work demonstrates that the microbiomes of corals in deep waters vary substantially across their ranges in accordance with depth and other environmental conditions. It reveals that the influence of depth on the ecology of mesophotic and deep-sea corals extends to its effects on their microbiomes which may have functional consequences. This work also identifies the distributions of microbes including potential parasites which can be used to inform restoration plans in response to the Deepwater Horizon oil spill.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":7.9,"publicationDate":"2024-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11165896/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141301883","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
Dynamics, diversity, and roles of bacterial transmission modes during the first asexual life stages of the freshwater sponge Spongilla lacustris. 淡水海绵 Spongilla lacustris 第一无性生命阶段细菌传播模式的动态、多样性和作用。
IF 7.9 2区 环境科学与生态学 Q2 Immunology and Microbiology Pub Date : 2024-06-08 DOI: 10.1186/s40793-024-00580-7
Benoit Paix, Elodie van der Valk, Nicole J de Voogd

Background: Sponge-associated bacteria play important roles in the physiology of their host, whose recruitment processes are crucial to maintain symbiotic associations. However, the acquisition of bacterial communities within freshwater sponges is still under explored. Spongilla lacustris is a model sponge widely distributed in European rivers and lakes, producing dormant cysts (named gemmules) for their asexual reproduction, before winter. Through an in vitro experiment, this study aims to describe the dynamics of bacterial communities and their transmission modes following the hatching of these gemmules.

Results: An overall change of bacterial β-diversity was observed through the ontology of the juvenile sponges. These temporal differences were potentially linked, first to the osculum acquisition and the development of a canal system, and then, the increasing colonization of the Chlorella-like photosymbionts. Gemmules hatching with a sterilized surface were found to have a more dispersed and less diverse microbiome, revealing the importance of gemmule epibacteria for the whole holobiont stability. These epibacteria were suggested to be vertically transmitted from the maternal tissues to the gemmule surface. Vertical transmission through the incorporation of bacterial communities inside of the gemmule, was also found as a dominant transmission mode, especially with the nitrogen fixers Terasakiellaceae. Finally, we showed that almost no ASVs were shared between the free-living community and the juveniles, suggesting that horizontal recruitment is unlikely to happen during the first stages of development. However, the free-living bacteria filtered are probably used as a source of nutrients, allowing an enrichment of copiotrophic bacteria already present within its microbiome.

Conclusions: This study brings new insight for a better understanding of the microbiome acquisition during the first stages of freshwater sponge development. We showed the importance of epibacterial communities on gemmules for the whole holobiont stability, and demonstrated the near absence of recruitment of free-living bacteria during the first stages.

背景:海绵相关细菌在宿主的生理过程中发挥着重要作用,其招募过程对于维持共生关系至关重要。然而,人们对淡水海绵内细菌群落的获取仍缺乏研究。漆海绵(Spongilla lacustris)是一种广泛分布于欧洲河流和湖泊中的海绵模型,在冬季到来之前会产生休眠囊胚(命名为gemules)进行无性繁殖。本研究旨在通过体外实验,描述这些宝石囊孵化后细菌群落的动态及其传播方式:结果:在幼年海绵的本体中观察到了细菌β多样性的整体变化。这些时间上的差异可能首先与窥视器的获得和管道系统的发展有关,然后与类似小球藻的光合共生体的定殖增加有关。在灭菌表面孵化的宝石虫的微生物群更分散,种类更少,这揭示了宝石虫附生细菌对整个全生物体稳定性的重要性。这些附生细菌被认为是从母体组织垂直传播到宝石表面的。我们还发现,通过将细菌群落纳入宝石内部进行垂直传播也是一种主要的传播方式,尤其是固氮菌 Terasakiellaceae。最后,我们发现自由生活群落和幼体之间几乎没有共享的 ASV,这表明在发育的最初阶段不太可能发生横向招募。不过,滤过的自由生活细菌可能被用作营养源,从而丰富了其微生物群落中已经存在的共养细菌:这项研究为更好地理解淡水海绵发育初期的微生物群获取带来了新的视角。我们表明了宝石囊上的表生细菌群落对整个全生物体稳定性的重要性,并证明了在最初阶段几乎没有自由生活细菌的招募。
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引用次数: 0
Environmental activity-based protein profiling for function-driven enzyme discovery from natural communities. 基于环境活性的蛋白质分析,从自然群落中发现功能驱动的酶。
IF 7.9 2区 环境科学与生态学 Q2 Immunology and Microbiology Pub Date : 2024-06-03 DOI: 10.1186/s40793-024-00577-2
Sabrina Ninck, Thomas Klaus, Tatiana V Kochetkova, Sarah P Esser, Leonard Sewald, Farnusch Kaschani, Christopher Bräsen, Alexander J Probst, Ilya V Kublanov, Bettina Siebers, Markus Kaiser

Background: Microbial communities are important drivers of global biogeochemical cycles, xenobiotic detoxification, as well as organic matter decomposition. Their major metabolic role in ecosystem functioning is ensured by a unique set of enzymes, providing a tremendous yet mostly hidden enzymatic potential. Exploring this enzymatic repertoire is therefore not only relevant for a better understanding of how microorganisms function in their natural environment, and thus for ecological research, but further turns microbial communities, in particular from extreme habitats, into a valuable resource for the discovery of novel enzymes with potential applications in biotechnology. Different strategies for their uncovering such as bioprospecting, which relies mainly on metagenomic approaches in combination with sequence-based bioinformatic analyses, have emerged; yet accurate function prediction of their proteomes and deciphering the in vivo activity of an enzyme remains challenging.

Results: Here, we present environmental activity-based protein profiling (eABPP), a multi-omics approach that extends genome-resolved metagenomics with mass spectrometry-based ABPP. This combination allows direct profiling of environmental community samples in their native habitat and the identification of active enzymes based on their function, even without sequence or structural homologies to annotated enzyme families. eABPP thus bridges the gap between environmental genomics, correct function annotation, and in vivo enzyme activity. As a showcase, we report the successful identification of active thermostable serine hydrolases from eABPP of natural microbial communities from two independent hot springs in Kamchatka, Russia.

Conclusions: By reporting enzyme activities within an ecosystem in their native state, we anticipate that eABPP will not only advance current methodological approaches to sequence homology-guided enzyme discovery from environmental ecosystems for subsequent biocatalyst development but also contributes to the ecological investigation of microbial community interactions by dissecting their underlying molecular mechanisms.

背景:微生物群落是全球生物地球化学循环、异生物解毒以及有机物分解的重要驱动力。它们在生态系统功能中的主要新陈代谢作用由一组独特的酶来保证,提供了巨大的但大多隐藏的酶潜能。因此,探索这套酶不仅有助于更好地了解微生物如何在自然环境中发挥作用,从而促进生态学研究,而且还能进一步将微生物群落(尤其是极端生境中的微生物群落)变成发现新型酶的宝贵资源,从而在生物技术领域获得潜在应用。目前已经出现了不同的发掘策略,如生物勘探,这主要依赖于元基因组方法与基于序列的生物信息学分析相结合;然而,对其蛋白质组进行准确的功能预测和破译酶的体内活性仍然具有挑战性:在这里,我们介绍了基于环境活性的蛋白质分析(eABPP),这是一种多组学方法,它将基因组解析的元基因组学与基于质谱的 ABPP 结合在一起。eABPP因此弥补了环境基因组学、正确的功能注释和体内酶活性之间的差距。作为展示,我们报告了从俄罗斯堪察加半岛两个独立温泉的天然微生物群落的 eABPP 中成功鉴定出活性恒温丝氨酸水解酶的情况:通过报告生态系统中原生状态下的酶活性,我们预计 eABPP 不仅能推进当前从环境生态系统中发现同源序列酶的方法,以促进后续生物催化剂的开发,而且还能通过剖析微生物群落相互作用的潜在分子机制,为微生物群落相互作用的生态学研究做出贡献。
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引用次数: 0
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Environmental Microbiome
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