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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 Q2 Immunology and Microbiology 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。
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引用次数: 0
Designing a synthetic microbial community through genome metabolic modeling to enhance plant-microbe interaction. 通过基因组代谢模型设计合成微生物群落以增强植物与微生物的相互作用。
IF 7.9 2区 环境科学与生态学 Q2 Immunology and Microbiology Pub Date : 2023-11-16 DOI: 10.1186/s40793-023-00536-3
Osiel S Gonçalves, Christopher J Creevey, Mateus F Santana

Background: Manipulating the rhizosphere microbial community through beneficial microorganism inoculation has gained interest in improving crop productivity and stress resistance. Synthetic microbial communities, known as SynComs, mimic natural microbial compositions while reducing the number of components. However, achieving this goal requires a comprehensive understanding of natural microbial communities and carefully selecting compatible microorganisms with colonization traits, which still pose challenges. In this study, we employed multi-genome metabolic modeling of 270 previously described metagenome-assembled genomes from Campos rupestres to design a synthetic microbial community to improve the yield of important crop plants.

Results: We used a targeted approach to select a minimal community (MinCom) encompassing essential compounds for microbial metabolism and compounds relevant to plant interactions. This resulted in a reduction of the initial community size by approximately 4.5-fold. Notably, the MinCom retained crucial genes associated with essential plant growth-promoting traits, such as iron acquisition, exopolysaccharide production, potassium solubilization, nitrogen fixation, GABA production, and IAA-related tryptophan metabolism. Furthermore, our in-silico selection for the SymComs, based on a comprehensive understanding of microbe-microbe-plant interactions, yielded a set of six hub species that displayed notable taxonomic novelty, including members of the Eremiobacterota and Verrucomicrobiota phyla.

Conclusion: Overall, the study contributes to the growing body of research on synthetic microbial communities and their potential to enhance agricultural practices. The insights gained from our in-silico approach and the selection of hub species pave the way for further investigations into the development of tailored microbial communities that can optimize crop productivity and improve stress resilience in agricultural systems.

背景:通过接种有益微生物调控根际微生物群落在提高作物产量和抗逆性方面已引起人们的兴趣。合成微生物群落,被称为SynComs,模仿天然微生物组成,同时减少成分的数量。然而,实现这一目标需要全面了解天然微生物群落,并仔细选择具有定殖特性的相容微生物,这仍然是一个挑战。在这项研究中,我们采用多基因组代谢建模方法,设计了一个合成微生物群落,以提高重要作物的产量。结果:我们采用有针对性的方法选择了一个包含微生物代谢必需化合物和植物相互作用相关化合物的最小群落(MinCom)。这导致最初的社区规模减少了大约4.5倍。值得注意的是,MinCom保留了与必需植物生长促进性状相关的关键基因,如铁获取、外多糖生产、钾增溶、固氮、GABA生产和iaa相关色氨酸代谢。此外,基于对微生物-微生物-植物相互作用的全面理解,我们对SymComs的计算机选择产生了一组6个中心物种,这些物种在分类上表现出显著的新颖性,包括Eremiobacterota和Verrucomicrobiota门的成员。结论:总体而言,该研究有助于对合成微生物群落及其对农业实践的潜力进行越来越多的研究。从我们的计算机方法和中心物种的选择中获得的见解为进一步研究定制微生物群落的发展铺平了道路,这些微生物群落可以优化作物生产力并提高农业系统的应激恢复能力。
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引用次数: 0
The gut microbiome mediates adaptation to scarce food in Coleoptera. 肠道微生物组介导鞘翅目对稀缺食物的适应。
IF 7.9 2区 环境科学与生态学 Q2 Immunology and Microbiology Pub Date : 2023-11-13 DOI: 10.1186/s40793-023-00537-2
Oana Teodora Moldovan, Alyssa A Carrell, Paul-Adrian Bulzu, Erika Levei, Ruxandra Bucur, Cristian Sitar, Luchiana Faur, Ionuț Cornel Mirea, Marin Șenilă, Oana Cadar, Mircea Podar

Beetles are ubiquitous cave invertebrates worldwide that adapted to scarce subterranean resources when they colonized caves. Here, we investigated the potential role of gut microbiota in the adaptation of beetles to caves from different climatic regions of the Carpathians. The beetles' microbiota was host-specific, reflecting phylogenetic and nutritional adaptation. The microbial community structure further resolved conspecific beetles by caves suggesting microbiota-host coevolution and influences by local environmental factors. The detritivore species hosted a variety of bacteria known to decompose and ferment organic matter, suggesting turnover and host cooperative digestion of the sedimentary microbiota and allochthonous-derived nutrients. The cave Carabidae, with strong mandibula, adapted to predation and scavenging of animal and plant remains, had distinct microbiota dominated by symbiotic lineages Spiroplasma or Wolbachia. All beetles had relatively high levels of fermentative Carnobacterium and Vagococcus involved in lipid accumulation and a reduction of metabolic activity, and both features characterize adaptation to caves.

甲虫是世界范围内普遍存在的洞穴无脊椎动物,当它们定居洞穴时,它们适应了稀缺的地下资源。在这里,我们研究了肠道微生物群在喀尔巴阡山脉不同气候区域的甲虫适应洞穴中的潜在作用。甲虫的微生物群是宿主特异性的,反映了系统发育和营养适应。微生物群落结构进一步通过洞穴解决了同种甲虫,表明微生物-宿主共同进化并受到当地环境因素的影响。这些食腐动物寄生着各种已知的分解和发酵有机物的细菌,表明沉积微生物群和外来来源的营养物质的周转和宿主的协同消化。洞穴甲壳类动物具有强壮的下颌骨,适应捕食和清除动物和植物的残骸,具有独特的微生物群,以共生谱系螺旋体或沃尔巴克氏体为主。所有的甲虫都有相对高水平的参与脂质积累和代谢活性降低的发酵性肉杆菌和迷走球菌,这两个特征都是适应洞穴的特征。
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引用次数: 0
Exploring the influence of climatic variables on mycobiome composition and community diversity in lichens: insights from structural equation modeling analysis. 探讨气候变量对地衣真菌生物群落组成和群落多样性的影响:结构方程建模分析的见解。
IF 7.9 2区 环境科学与生态学 Q2 Immunology and Microbiology Pub Date : 2023-10-27 DOI: 10.1186/s40793-023-00535-4
Jiho Yang, Jung-Jae Woo, Wonyong Kim, Seung-Yoon Oh, Jae-Seoun Hur

Background: Lichens are symbiotic organisms composed of a fungus and a photosynthetic partner, which are key ecological bioindicators due to their sensitivity to environmental changes. The endolichenic fungi (ELF) living inside lichen thalli, are an important but understudied component of playing crucial ecological roles such as nutrient cycling and protection against environmental stressors. Therefore ELF community investigation is vital for fostering sustainable ecosystems and leveraging their ecological benefits. Deciphering the intricate relationships between ELF and their lichen hosts, alongside the influence of environmental factors on these communities, presents a significant challenge in pinpointing the underlying drivers of community structure and diversity.

Results: Our research demonstrated that locational factors were the main drivers of the ELF community structure, rather than host haplotype. Several climatic factors affected the diversity of the ELF community and contributed to the prevalence of different types of fungal residents within the ELF community. A decrease in isothermality was associated with a greater prevalence of pathotrophic and saprotrophic fungi within the ELF community, resulting in an overall increase in community diversity. By conducting a structural equation modeling analysis, we identified a robust link between climatic variables, fungal trophic mode abundance, and the species diversity of the ELF community.

Conclusion: This study's discoveries emphasize the significance of examining climate-related factors when investigating ELF's structure and function. The connection between fungi and climate is intricate and complex, and can be influenced by various other factors. Investigating the potential for ELF to adapt to changing climatic conditions, as well as the potential effects of changes in ELF communities on lichen function, would be valuable research areas. We anticipate that our research results will establish a basis for numerous future ELF research projects and have a significant impact on the field.

背景:地衣是由真菌和光合伙伴组成的共生生物,由于它们对环境变化的敏感性,它们是关键的生态生物指标。生活在地衣铊中的地衣内生真菌(ELF)是一种重要但研究不足的组成部分,在发挥营养循环和抵御环境压力等关键生态作用方面发挥着重要作用。因此,ELF群落调查对于培育可持续生态系统和利用其生态效益至关重要。破译ELF与其地衣宿主之间的复杂关系,以及环境因素对这些群落的影响,在确定群落结构和多样性的潜在驱动因素方面提出了重大挑战。结果:我们的研究表明,位置因素是ELF群落结构的主要驱动因素,而不是宿主单倍型。几种气候因素影响了ELF群落的多样性,并导致ELF群落中不同类型真菌居民的流行。等温性的降低与ELF群落中病理营养型和腐生型真菌的更高流行率有关,导致群落多样性的总体增加。通过进行结构方程建模分析,我们确定了气候变量、真菌营养模式丰度和ELF群落物种多样性之间的有力联系。结论:本研究的发现强调了在研究ELF的结构和功能时考察气候相关因素的重要性。真菌和气候之间的联系是复杂而复杂的,并且可能受到各种其他因素的影响。研究ELF适应不断变化的气候条件的潜力,以及ELF群落变化对地衣功能的潜在影响,将是有价值的研究领域。我们预计,我们的研究成果将为未来的许多ELF研究项目奠定基础,并对该领域产生重大影响。
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引用次数: 0
Exploration of phyllosphere microbiomes in wheat varieties with differing aphid resistance. 抗蚜性不同小麦品种叶根球微生物组的研究。
IF 7.9 2区 环境科学与生态学 Q2 Immunology and Microbiology Pub Date : 2023-10-24 DOI: 10.1186/s40793-023-00534-5
Xinan Li, Chao Wang, Xun Zhu, Vardis Ntoukakis, Tomislav Cernava, Decai Jin

Background: Leaf-associated microbes play an important role in plant development and response to exogenous stress. Insect herbivores are known to alter the phyllosphere microbiome. However, whether the host plant's defense against insects is related to the phyllosphere microbiome remains mostly elusive. Here, we investigated bacterial communities in the phyllosphere and endosphere of eight wheat cultivars with differing aphid resistance, grown in the same farmland.

Results: The bacterial community in both the phyllosphere and endosphere showed significant differences among most wheat cultivars. The phyllosphere was connected to more complex and stable microbial networks than the endosphere in most wheat cultivars. Moreover, the genera Pantoea, Massilia, and Pseudomonas were found to play a major role in shaping the microbial community in the wheat phyllosphere. Additionally, wheat plants showed phenotype-specific associations with the genera Massilia and Pseudomonas. The abundance of the genus Exiguobacterium in the phyllosphere exhibited a significant negative correlation with the aphid hazard grade in the wheat plants.

Conclusion: Communities of leaf-associated microbes in wheat plants were mainly driven by the host genotype. Members of the genus Exiguobacterium may have adverse effects on wheat aphids. Our findings provide new clues supporting the development of aphid control strategies based on phyllosphere microbiome engineering.

背景:叶片相关微生物在植物发育和对外源胁迫的反应中发挥着重要作用。众所周知,昆虫食草动物会改变叶层微生物组。然而,寄主植物对昆虫的防御是否与叶层微生物组有关,目前仍不清楚。在这里,我们调查了生长在同一农田中的八个不同抗蚜性的小麦品种的叶层和内层中的细菌群落。结果:大多数小麦品种叶层和内层细菌群落存在显著差异。在大多数小麦品种中,叶圈与比内圈更复杂、更稳定的微生物网络相连。此外,Pantoea属、Massilia属和假单胞菌属在小麦叶层微生物群落的形成中发挥着重要作用。此外,小麦植株表现出和Massilia属和假单胞菌属的表型特异性关联。小麦叶层中Exiguobacterium属的丰度与蚜虫危害程度呈显著负相关。结论:小麦叶片相关微生物群落主要由寄主基因型驱动。Exiguobacterium属的成员可能对麦蚜产生不利影响。我们的发现为开发基于叶际微生物组工程的蚜虫控制策略提供了新的线索。
{"title":"Exploration of phyllosphere microbiomes in wheat varieties with differing aphid resistance.","authors":"Xinan Li, Chao Wang, Xun Zhu, Vardis Ntoukakis, Tomislav Cernava, Decai Jin","doi":"10.1186/s40793-023-00534-5","DOIUrl":"10.1186/s40793-023-00534-5","url":null,"abstract":"<p><strong>Background: </strong>Leaf-associated microbes play an important role in plant development and response to exogenous stress. Insect herbivores are known to alter the phyllosphere microbiome. However, whether the host plant's defense against insects is related to the phyllosphere microbiome remains mostly elusive. Here, we investigated bacterial communities in the phyllosphere and endosphere of eight wheat cultivars with differing aphid resistance, grown in the same farmland.</p><p><strong>Results: </strong>The bacterial community in both the phyllosphere and endosphere showed significant differences among most wheat cultivars. The phyllosphere was connected to more complex and stable microbial networks than the endosphere in most wheat cultivars. Moreover, the genera Pantoea, Massilia, and Pseudomonas were found to play a major role in shaping the microbial community in the wheat phyllosphere. Additionally, wheat plants showed phenotype-specific associations with the genera Massilia and Pseudomonas. The abundance of the genus Exiguobacterium in the phyllosphere exhibited a significant negative correlation with the aphid hazard grade in the wheat plants.</p><p><strong>Conclusion: </strong>Communities of leaf-associated microbes in wheat plants were mainly driven by the host genotype. Members of the genus Exiguobacterium may have adverse effects on wheat aphids. Our findings provide new clues supporting the development of aphid control strategies based on phyllosphere microbiome engineering.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":7.9,"publicationDate":"2023-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10594911/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50159018","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
Distinct coral environments shape the dynamic of planktonic Vibrio spp. 不同的珊瑚环境决定了浮游弧菌的动态。
IF 7.9 2区 环境科学与生态学 Q2 Immunology and Microbiology Pub Date : 2023-10-23 DOI: 10.1186/s40793-023-00532-7
Wenbin Zhao, Xing Chen, Ronghua Liu, Peng Tian, Wentao Niu, Xiao-Hua Zhang, Jiwen Liu, Xiaolei Wang

Background: Coral reefs are one of the most biodiverse and productive ecosystems, providing habitat for a vast of species. Reef-building scleractinian corals with a symbiotic microbiome, including bacteria, archaea, viruses and eukaryotic microbes, are referred to coral holobionts. Among them, coral diseases, mainly caused by Vibrio spp., have significantly contributed to the loss of coral cover and diversity. Habitat filtering across the globe has led to a variety structure of marine bacterial communities. Coral species, quantity and characteristics are significant differences between the Xisha Islands and Daya Bay (Guangdong Province). Thus, the Vibrio communities may be distinct between coral rich and poor areas.

Results: Through comparison of Vibrio dynamics between coral-rich (Xisha Islands) and coral-poor (Daya Bay) locations, we uncovered differences in Vibrio abundance, diversity, community composition and assembly mechanisms associated with corals. The higher abundance of Vibrio in coral rich areas may indicate a strong interaction between vibrios and corals. V. campbellii, Paraphotobacterium marinum and V. caribbeanicus were widely distributed in both coral rich and poor areas, likely indicating weak species specificity in the coral-stimulated growth of Vibrio. Random-forest prediction revealed Vibrio species and Photobacterium species as potential microbial indicators in the coral rich and coral poor areas, respectively. Ecological drift rather than selection governed the Vibrio community assembly in the Xisha Islands. Comparatively, homogenizing selection was more important for the Daya Bay community, which may reflect a role of habitat filtration.

Conclusion: This study revealed the different distribution pattern and assembly mechanism of Vibrio spp. between coral rich and poor areas, providing the background data for the research of Vibrio community in coral reef areas and may help the protection of coral reef at the biological level. The main reasons for the difference were different number and species of corals, environmental (e.g., temperature) and spatial factors. It reflected the strong interaction between Vibrio and corals, and provided a new perspective for the investigation of Vibrio in coral reef ecosystem.

背景:珊瑚礁是生物多样性和生产力最高的生态系统之一,为大量物种提供了栖息地。具有共生微生物组的造礁巩膜珊瑚,包括细菌、古菌、病毒和真核微生物,被称为珊瑚全生物。其中,主要由弧菌引起的珊瑚疾病对珊瑚覆盖和多样性的丧失起到了重要作用。栖息地在全球范围内的过滤导致了海洋细菌群落的多样性结构。西沙群岛与广东大亚湾的珊瑚种类、数量和特征存在显著差异。因此,弧菌群落在珊瑚丰富和珊瑚贫乏地区之间可能是不同的。结果:通过比较富含珊瑚(西沙群岛)和缺乏珊瑚(大亚湾)地区的弧菌动力学,我们发现了与珊瑚相关的弧菌丰度、多样性、群落组成和组装机制的差异。在珊瑚丰富的地区,弧菌的丰度较高,这可能表明弧菌与珊瑚之间存在强烈的相互作用。campbellii弧菌、海洋副光杆菌和加勒比弧菌广泛分布在珊瑚富集区和珊瑚贫乏区,这可能表明珊瑚刺激的弧菌生长的物种特异性较弱。随机森林预测显示,弧菌和光细菌分别是珊瑚丰富和珊瑚贫乏地区的潜在微生物指标。西沙群岛弧菌群落的聚集是由生态漂移而非选择决定的。相比之下,均质化选择对大亚湾群落更为重要,这可能反映了栖息地过滤的作用。结论:本研究揭示了富珊瑚区和贫珊瑚区弧菌的不同分布模式和组装机制,为珊瑚礁区弧菌群落的研究提供了背景数据,有助于珊瑚礁的生物保护。造成差异的主要原因是珊瑚的数量和种类不同、环境(如温度)和空间因素。它反映了弧菌与珊瑚之间的强烈相互作用,为研究珊瑚礁生态系统中的弧菌提供了新的视角。
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引用次数: 0
Successional action of Bacteroidota and Firmicutes in decomposing straw polymers in a paddy soil. 拟杆菌门和厚壁菌门在水稻土中分解秸秆聚合物的后续作用。
IF 7.9 2区 环境科学与生态学 Q2 Immunology and Microbiology Pub Date : 2023-10-14 DOI: 10.1186/s40793-023-00533-6
Junjie Huang, Kailin Gao, Lu Yang, Yahai Lu

Background: Decomposition of plant biomass is vital for carbon cycling in terrestrial ecosystems. In waterlogged soils including paddy fields and natural wetlands, plant biomass degradation generates the largest natural source of global methane emission. However, the intricate process of plant biomass degradation by diverse soil microorganisms remains poorly characterized. Here we report a chemical and metagenomic investigation into the mechanism of straw decomposition in a paddy soil.

Results: The chemical analysis of 16-day soil microcosm incubation revealed that straw decomposition could be divided into two stages based on the dynamics of methane, short chain fatty acids, dissolved organic carbon and monosaccharides. Metagenomic analysis revealed that the relative abundance of glucoside hydrolase (GH) encoding genes for cellulose decomposition increased rapidly during the initial stage (3-7 days), while genes involved in hemicellulose decomposition increased in the later stage (7-16 days). The increase of cellulose GH genes in initial stage was derived mainly from Firmicutes while Bacteroidota contributed mostly to the later stage increase of hemicellulose GH genes. Flagella assembly genes were prevalent in Firmicutes but scarce in Bacteroidota. Wood-Ljungdahl pathway (WLP) was present in Firmicutes but not detected in Bacteroidota. Overall, Bacteroidota contained the largest proportion of total GHs and the highest number of carbohydrate active enzymes gene clusters in our paddy soil metagenomes. The strong capacity of the Bacteroidota phylum to degrade straw polymers was specifically attributed to Bacteroidales and Chitinophagales orders, the latter has not been previously recognized.

Conclusions: This study revealed a collaborating sequential contribution of microbial taxa and functional genes in the decomposition of straw residues in a paddy soil. Firmicutes with the property of mobility, WLP and cellulose decomposition could be mostly involved in the initial breakdown of straw polymers, while Bacteroidota became abundant and possibly responsible for the decomposition of hemicellulosic polymers during the later stage.

背景:植物生物量的分解对陆地生态系统的碳循环至关重要。在包括稻田和自然湿地在内的积水土壤中,植物生物量退化是全球甲烷排放的最大自然来源。然而,不同土壤微生物降解植物生物量的复杂过程仍然缺乏特征。在这里,我们报道了一项关于稻草在水稻土中分解机制的化学和宏基因组研究。结果:土壤微宇宙培养16天的化学分析表明,秸秆分解可根据甲烷、短链脂肪酸、溶解有机碳和单糖的动态分为两个阶段。宏基因组分析显示,编码纤维素分解基因的葡萄糖苷水解酶(GH)的相对丰度在初始阶段(3-7天)迅速增加,而参与半纤维素分解的基因在后期(7-16天)增加。初期纤维素GH基因的增加主要来源于厚壁菌门,而拟杆菌门对后期半纤维素GH基因增加的贡献很大。Flagella组装基因在厚壁菌门中普遍存在,但在拟杆菌门中很少。Wood-Ljungdahl通路(WLP)存在于厚壁菌门中,但在拟杆菌门中未检测到。总体而言,在我们的水稻土壤宏基因组中,拟杆菌门含有最大比例的总GHs和最高数量的碳水化合物活性酶基因簇。拟杆菌门降解秸秆聚合物的强大能力被专门归因于拟杆菌目和几丁质目,后者以前尚未得到认可。结论:本研究揭示了微生物类群和功能基因在水稻土秸秆残留物分解中的协同序列贡献。具有移动性、WLP和纤维素分解特性的厚壁菌门可能主要参与秸秆聚合物的初始分解,而拟杆菌门变得丰富,并可能负责后期半纤维素聚合物的分解。
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引用次数: 0
Distinct patterns of distribution, community assembly and cross-domain co-occurrence of planktonic archaea in four major estuaries of China. 中国四个主要河口浮游古菌的分布、群落聚集和跨域共现模式不同。
IF 6.2 2区 环境科学与生态学 Q1 GENETICS & HEREDITY Pub Date : 2023-10-07 DOI: 10.1186/s40793-023-00530-9
Xuya Hu, Yujie Huang, Gaoke Gu, Hanjing Hu, Huizhen Yan, Huajun Zhang, Rui Zhang, Demin Zhang, Kai Wang

Background: Archaea are key mediators of estuarine biogeochemical cycles, but comprehensive studies comparing archaeal communities among multiple estuaries with unified experimental protocols during the same sampling periods are scarce. Here, we investigated the distribution, community assembly, and cross-domain microbial co-occurrence of archaea in surface waters across four major estuaries (Yellow River, Yangtze River, Qiantang River, and Pearl River) of China cross climatic zones (~ 1,800 km) during the winter and summer cruises.

Results: The relative abundance of archaea in the prokaryotic community and archaeal community composition varied with estuaries, seasons, and stations (reflecting local environmental changes such as salinity). Archaeal communities in four estuaries were overall predominated by ammonia-oxidizing archaea (AOA) (aka. Marine Group (MG) I; primarily Nitrosopumilus), while the genus Poseidonia of Poseidoniales (aka. MGII) was occasionally predominant in Pearl River estuary. The cross-estuary dispersal of archaea was largely limited and the assembly mechanism of archaea varied with estuaries in the winter cruise, while selection governed archaeal assembly in all estuaries in the summer cruise. Although the majority of archaea taxa in microbial networks were peripherals and/or connectors, extensive and distinct cross-domain associations of archaea with bacteria were found across the estuaries, with AOA as the most crucial archaeal group. Furthermore, the expanded associations of MGII taxa with heterotrophic bacteria were observed, speculatively indicating the endogenous demand for co-processing high amount and diversity of organic matters in the estuarine ecosystem highly impacted by terrestrial/anthropogenic input, which is worthy of further study.

Conclusions: Our results highlight the lack of common patterns in the dynamics of estuarine archaeal communities along the geographic gradient, expanding the understanding of roles of archaea in microbial networks of this highly dynamic ecosystem.

背景:古菌是河口生物地球化学循环的关键介质,但在同一采样期内,用统一的实验方案比较多个河口古菌群落的综合研究很少。在这里,我们调查了中国四个主要河口(黄河、长江、钱塘江和珠江)地表水中古菌的分布、群落聚集和跨领域微生物共现(~ 1800公里)。结果:原核群落中古菌的相对丰度和古菌群落组成因河口、季节和站点而异(反映了盐度等当地环境变化)。四个河口的古菌群落总体上以氨氧化古菌(AOA)为主(又名海洋群(MG)I;主要为Nitrosopumilus),而Poseidoniales的Poseidonia属(又名MGII)偶尔在珠江口占主导地位。古菌的跨河口扩散在很大程度上受到限制,古菌的聚集机制在冬季巡航中因河口而异,而在夏季巡航中,所有河口的古菌聚集都受到选择的支配。尽管微生物网络中的大多数古菌分类群是外围和/或连接体,但在河口发现了广泛而独特的古菌与细菌的跨域关联,其中AOA是最重要的古菌群。此外,观察到MGII分类群与异养细菌的扩展关联,推测性地表明,在受到陆地/人为输入高度影响的河口生态系统中,共处理大量和多样性有机物的内源性需求值得进一步研究。结论:我们的研究结果突出了河口古菌群落在地理梯度上的动力学缺乏共同模式,扩大了对古菌在这个高度动态的生态系统的微生物网络中的作用的理解。
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引用次数: 0
Compost, plants and endophytes versus metal contamination: choice of a restoration strategy steers the microbiome in polymetallic mine waste. 堆肥、植物和内生菌与金属污染:恢复策略的选择引导多金属矿山废物中的微生物组。
IF 7.9 2区 环境科学与生态学 Q2 Immunology and Microbiology Pub Date : 2023-10-07 DOI: 10.1186/s40793-023-00528-3
Martina Kracmarova-Farren, Jakub Papik, Ondrej Uhlik, John Freeman, Andrea Foster, Mary-Cathrine Leewis, Courtney Creamer

Finding solutions for the remediation and restoration of abandoned mining areas is of great environmental importance as they pose a risk to ecosystem health. In this study, our aim was to determine how remediation strategies with (i) compost amendment, (ii) planting a metal-tolerant grass Bouteloua curtipendula, and (iii) its inoculation with beneficial endophytes influenced the microbiome of metal-contaminated tailings originating from the abandoned Blue Nose Mine, SE Arizona, near Patagonia (USA). We conducted an indoor microcosm experiment followed by a metataxonomic analysis of the mine tailings, compost, and root samples. Our results showed that each remediation strategy promoted a distinct pattern of microbial community structure in the mine tailings, which correlated with changes in their chemical properties. The combination of compost amendment and endophyte inoculation led to the highest prokaryotic diversity and total nitrogen and organic carbon, but also induced shifts in microbial community structure that significantly correlated with an enhanced potential for mobilization of Cu and Sb. Our findings show that soil health metrics (total nitrogen, organic carbon and pH) improved, and microbial community changed, due to organic matter input and endophyte inoculation, which enhanced metal leaching from the mine waste and potentially increased environmental risks posed by Cu and Sb. We further emphasize that because the initial choice of remediation strategy can significantly impact trace element mobility via modulation of both soil chemistry and microbial communities, site specific, bench-scale preliminary tests, as reported here, can help determine the potential risk of a chosen strategy.

寻找修复和恢复废弃矿区的解决方案对环境具有重要意义,因为它们对生态系统健康构成风险。在这项研究中,我们的目的是确定(i)堆肥改良、(ii)种植耐金属草Bouteloua curtipendula和(iii)接种有益内生菌的修复策略如何影响源自巴塔哥尼亚(美国)附近亚利桑那州东南部废弃蓝鼻矿的金属污染尾矿的微生物组。我们进行了一个室内微观实验,然后对尾矿、堆肥和根样本进行了跖骨组学分析。我们的研究结果表明,每种修复策略都促进了尾矿中微生物群落结构的独特模式,这与尾矿化学性质的变化有关。堆肥改良和内生菌接种的结合导致了最高的原核生物多样性、总氮和有机碳,但也诱导了微生物群落结构的变化,这与Cu和Sb动员潜力的增强显著相关。我们的研究结果表明,土壤健康指标(总氮、有机碳和pH)得到了改善,由于有机物的输入和内生菌的接种,微生物群落发生了变化,这增强了矿山废物中的金属浸出,并可能增加Cu和Sb带来的环境风险。我们进一步强调,由于最初选择的修复策略可以通过调节土壤化学和微生物群落来显著影响微量元素的迁移,如本文所述,针对特定地点的实验室规模初步测试可以帮助确定所选策略的潜在风险。
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引用次数: 1
Fungal community inside lichen: a curious case of sparse diversity and high modularity. 地衣内部的真菌群落:稀疏多样性和高度模块化的奇怪案例。
IF 7.9 2区 环境科学与生态学 Q2 Immunology and Microbiology Pub Date : 2023-10-03 DOI: 10.1186/s40793-023-00531-8
Jiho Yang, Jung-Jae Woo, Seung-Yoon Oh, Wonyong Kim, Jae-Seoun Hur

Background: Lichens represent not only the mutualism of fungal and photosynthetic partners but also are composed of microbial consortium harboring diverse fungi known as endolichenic fungi. While endolichenic fungi are known to exert a remarkable influence on lichen ecology through their crucial roles in nutrient cycling, bioprospecting and biodiversity, the enigmatic community structures of these fungal inhabitants remain shrouded in mystery, awaiting further exploration and discovery. To address knowledge gap, we conducted metabarcoding on two lichens using 18S gene amplification, Dirinara applanta and Parmotrema tinctorum, and compared their microbial communities to those found in the pine bark to which the lichens were attached. Our hypothesis was that the endolichenic communities would exhibit distinct diversity patterns, community structures, network structures, and specialist composition compared to the surrounding epiphytic community.

Results: Our investigation has shed light on the clear demarcation between the endolichenic and epiphytic fungal communities, as they exhibit markedly different characteristics that set them apart from each other. This research demonstrated that the endolichenic communities are less diverse as compared to the epiphytic communities. Through community similarity analysis, we observed that two endolichenic communities are more similar to each other in terms of community composition than with the adjacent epiphytic communities. Moreover, we unveiled a striking contrast in the network structures between the endolichenic and epiphytic communities, as the former displayed a more modular and less nested features that is evocative of a potent host-filtration mechanism.

Conclusions: Through our investigation, we have discovered that lichens harbor less intricate and interconnected fungal communities compared to the neighboring epiphytic environment. These observations provide valuable insights into the metagenomic architecture of lichens and offer a tantalizing glimpse into the unique mycobiome.

背景:地衣不仅代表真菌和光合伙伴的互惠共生,而且由携带多种真菌的微生物群落组成,这些真菌被称为内地衣真菌。众所周知,地衣内生真菌通过其在营养循环、生物勘探和生物多样性中的关键作用,对地衣生态产生了显著影响,但这些真菌群落的神秘结构仍然笼罩在神秘之中,等待进一步的探索和发现。为了解决知识差距,我们使用18S基因扩增对两种地衣进行了代谢编码,Dirinara applanta和Parmotrema tinctorum,并将它们的微生物群落与地衣附着的松树皮中发现的微生物群落进行了比较。我们的假设是,与周围的附生群落相比,内生地衣群落将表现出不同的多样性模式、群落结构、网络结构和专家组成。结果:我们的研究清楚地划分了地衣内真菌群落和附生真菌群落,因为它们表现出明显不同的特征,使它们彼此不同。这项研究表明,与附生群落相比,内生地衣群落的多样性较低。通过群落相似性分析,我们观察到两个内生地衣群落在群落组成方面比相邻的附生群落更相似。此外,我们揭示了地衣内生群落和附生群落之间网络结构的惊人对比,因为前者表现出更模块化和更少嵌套的特征,这唤起了强大的宿主过滤机制。结论:通过我们的调查,我们发现与邻近的附生环境相比,地衣的真菌群落不那么复杂和相互关联。这些观察结果为地衣的宏基因组结构提供了宝贵的见解,并为独特的真菌生物群落提供了诱人的一瞥。
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引用次数: 0
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Environmental Microbiome
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