MICROBIAL ECOLOGY微生物生态学
MICROBIAL ECOLOGY(英文缩写 MICROB ECOL),ISSN 0095-3628,eISSN 1432-184X,中文译名:微生物生态学 是一本学术期刊。本页汇总该期刊的最新影响因子、分区信息以及最新收录于 PubMed 的文献,帮助您快速了解期刊全貌。
发文量统计区间：2025-11-01 至 2026-10-31，按本站收录文献的发表日期统计。
期刊介绍
历年影响因子趋势
| JCR 数据年份 | 影响因子 | JCR 分区 |
|---|---|---|
| 2021 | 4.192 | Q1 |
| 2022 | 3.600 | Q1 |
| 2023 | 3.300 | Q1 |
| 2024 | 4.000 | Q1 |
| 2025 | 4.300 | Q1 |
MICROBIAL ECOLOGY 最新收录文献
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1. Chronic Nitrogen Deposition Alters Diazotrophic Community Composition, Reduces Biological Nitrogen Fixation, and Restructures Fungal-Diazotroph CO-Occurrence Networks in Deadwood.
1. 长期氮沉降改变枯木中固氮微生物群落组成、降低生物固氮并重塑真菌-固氮菌共现网络PMID:日期:2026-08-01Biological nitrogen fixation (BNF) by diazotrophs contributes to increasing nitrogen (N) availability in nutrient-poor deadwood during the decomposition process. However, chronically elevated atmospheric N deposition may increase N availability, thereby reshaping diazotrophic community and suppressing BNF. We simulated high N deposition by repeatedly applying ammonium-nitrate solution to deadwood of 13 tree species over 9 years (N addition) and compared diazotrophic community composition and BNF rates with untreated controls. Deadwood N concentrations increased over time in both control and N addition, with N addition resulting in higher N concentrations at the final sampling, although significant treatment effects were detected only in Tilia and Pinus. Chronic high-N addition was associated with reduced BNF activity, with significant suppression primarily observed in coniferous deadwood, while responses among broadleaved species were weak, variable, or absent. The N addition altered diazotroph richness and community composition by increasing the abundance of Bradyrhizobium and by reducing Methylocapsa across all tree species. Under N addition, BNF correlated positively with nifH gene copy numbers in broadleaved deadwood but negatively in coniferous deadwood. Co-occurrence networks were more interconnected and modular under N addition, with diazotrophs (e.g., Azospirillum) central in broadleaved deadwood and fungi (e.g., Meliniomyces, Athelia) central in coniferous deadwood. Tree clade (coniferous vs. broadleaved) strongly shaped richness and community response, with broadleaved and coniferous species showing distinct patterns.Overall, the largely robust diversity and community composition of diazotrophs and BNF activity under high N addition suggest that moderately increasing N deposition has little influence on fungal deadwood decomposition and the function of deadwood as a carbon pool in forest ecosystems.
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2. Retraction Note: Purification and Characterization of Desferrioxamine B of Pseudomonas fluorescens and Its Application to Improve Oil Content, Nutrient Uptake, and Plant Growth in Peanuts.
2. 撤稿说明：荧光假单胞菌去铁胺B的纯化与表征及其在提高花生含油量、养分吸收和植物生长中的应用PMID:日期:2026-07-25该文献暂无摘要。
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3. Effects of Culture History and Algal Taxonomy on Bacterial Communities in Long-maintained Filamentous Green Algae.
3. 培养历史与藻类分类对长期保存的丝状绿藻中细菌群落的影响PMID:日期:2026-07-22Algal cultures are widely used to study algae-bacteria interactions, yet the relative roles of algal taxonomy, culturing environment, and historical contingency in shaping bacterial communities of long-maintained monoalgal cultures remain unclear. In a two-stage experimental design, we used 16 S rRNA metabarcoding to first profile the bacterial communities of 14 filamentous freshwater algal strains from three orders (Chaetophorales, Oedogoniales, Zygnematales) maintained in two distinct culture collections, and then, in a second experiment to test community mixing using a co-culture and re-isolation design with two algal strains (Stigeoclonium sp. and Oedogonium sp.). The 14-strain profiling showed that bacterial communities were broadly similar at higher taxonomic ranks, with many shared orders within Pseudomonadota, whereas composition at the ASV level was largely algal-strain-specific. Ordination of phylogeny-aware UniFrac distances showed that culture collection of origin explained more variation in community composition than algal order, an effect reduced but not eliminated after standardizing the culture medium. The co-culture and re-isolation experiment showed that the two algal strains exchanged many bacterial community members, yet algal strain identity remained detectable after re-isolation. These results support a framework where culture history results in strain-specific ASV-level composition within recurrent higher-rank structure, and where algal-strain-specific effects on bacterial community composition become evident when cultures are exposed to a shared bacterial pool. Co-culture followed by algal re-isolation offers a practical approach to examine the persistence of algal-culture bacterial communities under mixing and may help identify candidate bacterial partners with potentially strong host-specific interactions without requiring axenic hosts.
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4. Bacterial and Green Algal Communities of Norwegian Birch Tree Bark.
4. 挪威白桦树皮的细菌和绿藻群落PMID:日期:2026-07-21[中文摘要] 树皮栖息着独特的微生物群落，与其他植物组织以及大型附生植物的微生物关联群落截然不同。这些树皮附生群落（corticolous communities）是树木相关食物网的重要组成部分。然而，影响树皮附生微生物多样性的因素研究不足。我们采用扩增子测序技术，对挪威南部三个氮沉降历史不同的地点中定殖于桦树树皮的细菌和氣生藻类群落进行了表征和比较。在每个地点内，我们研究了树皮附生群落与树干上位置变化之间的关联，包括朝向（北向与南向）、高度和树干直径。尽管三个地点中最丰富的细菌和藻类分类单元相似，但地点之间存在明显差异。朝向在最具海洋性且开阔的地点具有强烈影响，北向较南向蓝细菌丰度增加。我们观察到，在历史氮沉降最低的地点，固氮蓝细菌丰度较高；相应地，在历史氮沉降最高的地点，非固氮绿藻丰度较高。总体而言，细菌和藻类群落呈现相似的模式，共现网络分析（co-occurrence network analysis）揭示藻类分类单元散布于细菌簇之间。本研究首次对桦树——挪威最常见且生态最重要的树种之一——的细菌和氣生藻类树皮关联群落进行了表征。我们的结果进一步充实了越来越多的文献，表明树皮承载着复杂的微生物群落，且群落随地点而变化。
[英文摘要] Tree bark hosts a unique community of microorganisms, distinct from that of other plant tissues and from the microbial associates of macrophytic epiphytes. These corticolous communities are important components of tree-associated food webs. However, the factors influencing corticolous microbial diversity are understudied. We used amplicon sequencing to characterise and compare the bacterial and aerophytic algal communities colonising the bark of birch trees at three sites in southern Norway with differing histories of nitrogen deposition. Within each site, we investigated associations between the corticolous community and variation in placement on the trunk, including north-facing vs. south-facing aspect, height and trunk diameter. While the most abundant bacterial and algal taxa were similar across the three sites, there were clear differences among sites. Aspect had a strong effect at the most oceanic and open site, with increased abundance of cyanobacteria at northern compared to southern aspects. We observed a higher abundance of nitrogen-fixing cyanobacteria at the site where historical nitrogen deposition had been lowest and correspondingly higher abundance of non-diazotrophic green algae where historical nitrogen deposition had been highest. Generally, the bacterial and algal communities followed similar patterns and co-occurrence network analysis revealed that algal taxa were interspersed among bacterial clusters. Our study provides the first characterisation of both the bacterial and aerophytic algal bark-associated communities of birch, one of the most common and ecologically important trees in Norway. Our results add to the growing body of literature demonstrating that tree bark supports a complex microbial community that varies among sites.
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5. Beyond Dominant Symbionts: Low-Abundance Taxa Govern Microbial Network Topology in Sympatric Ticks.
5. 超越优势共生体：低丰度类群主导同域蜱虫中的微生物网络拓扑结构PMID:日期:2026-07-20[中文摘要] 蜱是专性吸血节肢动物，也是多种细菌、寄生虫和病毒病原体的主要传播媒介。它们携带着复杂的微生物群落，这些群落对其生物学特性、适合度以及与病原体的相互作用具有关键影响。本研究采用扩增子序列变体（ASV）分辨率的16S rRNA基因扩增子测序，结合共现网络分析，对在西班牙哈恩省卡索拉、塞古拉和拉斯比利亚斯自然公园采集的待血成蜱的细菌群落进行了表征。共分析了83只成蜱（27只雄性和56只雌性），代表6个同域物种：边缘革蜱（Dermacentor marginatus，n=39）、刻点血蜱（Haemaphysalis punctata，n=9）、沟纹血蜱（H. sulcata，n=15）、卢西塔尼亚璃眼蜱（Hyalomma lusitanicum，n=7）、蓖麻硬蜱广义种（Ixodes ricinus s. l.，n=2）和囊状扇头蜱（Rhipicephalus bursa，n=11）。经过严格的质量过滤后，共获得377万条高质量序列读数，并解析为407个ASV。由于V3-V4区域在物种水平区分上存在固有的分辨率限制，分类学归属被保守地合并至属水平（101个细菌属）。在所有蜱种中，细菌组以假单胞菌门（Pseudomonadota）为绝对优势（98.6%），种间差异主要由专性共生菌的变异驱动。柯克斯体属（Coxiella）相关ASV在多个蜱种中占优势，而卢西塔尼亚璃眼蜱则表现出弗朗西斯菌属（Francisella）的强烈优势和候选Midichloria菌的次要代表。α多样性和β多样性分析揭示了由宿主身份塑造的独特组成模式，其中边缘革蜱和囊状扇头蜱的离散度较低，而璃眼蜱属和血蜱属个体间的变异性较大。基于Spearman的共现网络分析表明，跨蜱种存在高度合作性和模块化结构（>98%正相关）。值得注意的是，优势内共生菌（柯克斯体属、立克次体属和弗朗西斯菌属）占据网络中的外围或弱连接位置。相比之下，生态连通性由一组独特的低丰度类群所主导，包括玫瑰单胞菌属（Roseomonas）、Friedmanniella、甲基杆菌属（Methylobacterium）、鞘氨醇单胞菌属（Sphingomonas）、Aureimonas、Conexibacter、Marmoricola、分枝杆菌属（Mycobacterium）和类诺卡氏菌属（Nocardioides），它们作为中心枢纽桥接网络模块，这一拓扑结构通过在边缘革蜱队列中进行的独立、组成感知（SparCC）再分析得到了稳健验证。这些比较研究结果表明，蜱微生物组中存在丰度与连通性之间的功能性解耦，凸显了“稀有微生物组”如何驱动同域宿主物种间微生物群落的拓扑组织和潜在稳定性。
[英文摘要] Ticks are obligate hematophagous arthropods and major vectors of diverse bacterial, parasitic, and viral pathogens. They host complex microbial communities that critically influence their biology, fitness, and interactions with pathogens. Using 16 S rRNA gene amplicon sequencing at the amplicon sequence variant (ASV) resolution combined with co-occurrence network analysis, we characterized the bacterial communities of questing adult ticks collected in the Cazorla, Segura y Las Villas Natural Park (Jaén, Spain). A total of 83 adult ticks (27 males and 56 females) representing six sympatric species, Dermacentor marginatus (n = 39), Haemaphysalis punctata (n = 9), H. sulcata (n = 15), Hyalomma lusitanicum (n = 7), Ixodes ricinus s. l. (n = 2), and Rhipicephalus bursa (n = 11), were analyzed. After stringent quality filtering, 3.77 million high-quality reads were recovered and resolved into 407 ASVs. Due to the inherent resolution limits of the V3-V4 region for species-level discrimination, taxonomic assignments were conservatively consolidated at the genus level (101 bacterial genera). Across all tick species, the bacteriome was heavily dominated by Pseudomonadota (98.6%), with species-specific differences primarily driven by variation in obligate symbionts. Coxiella-associated ASVs predominated in multiple tick species, whereas H. lusitanicum exhibited strong dominance by Francisella and secondary representation of Candidatus Midichloria. Alpha and beta diversity analyses revealed distinct compositional patterns shaped by host identity, with lower dispersion observed in D. marginatus and R. bursa, and greater variability among Hyalomma and Haemaphysalis individuals. Spearman-based co-occurrence network analysis indicated a highly cooperative and modular structure (> 98% positive correlations) across tick species. Notably, dominant endosymbionts (Coxiella, Rickettsia, and Francisella) occupied peripheral or weakly connected positions within the networks. In contrast, ecological connectivity was governed by a distinct set of low-abundance taxa, including Roseomonas, Friedmanniella, Methylobacterium, Sphingomonas, Aureimonas, Conexibacter, Marmoricola, Mycobacterium, and Nocardioides, which acted as central hubs bridging network modules, a topology robustly validated by an independent, composition-aware (SparCC) reanalysis within the D. marginatus cohort. These comparative findings demonstrate a functional decoupling between abundance and connectivity in tick microbiomes, highlighting how the "rare microbiome" can drive the topological organization and potential stability of microbial communities across sympatric host species.
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6. Microbial Diversity, Structure and Predicted Carbon-cycling Pathways Show Partial Convergence in Restored and Natural Salt Marshes in Venice Lagoon.
6. 微生物多样性、结构及预测的碳循环途径在威尼斯潟湖修复与自然盐沼中呈现部分趋同PMID:日期:2026-07-15Salt marshes are increasingly restored following widespread degradation, yet the responses of sediment microbial communities to restoration remain poorly understood, despite their central role in ecosystem functioning. We compared microbial diversity, composition, structure and predicted function between natural (N) and two types of restored salt marshes in Venice lagoon, Italy: marshes restored with tidal creeks (RC), favouring a more natural tidal exchange and creek formation at the low marsh, and marshes restored with barriers (RB), which constrain tidal flow. We analysed sediment microbial communities in the three dominant habitat types of each marsh (unvegetated low marsh, vegetated low marsh, vegetated mid marsh) by amplicon sequencing of the V4 and V5 hypervariable regions of the 16 S rRNA gene. Microbial diversity was similar across natural and restored salt marshes, but community composition and structure were different. Natural marshes were characterised by higher abundances of taxa associated with sulphate reduction and organic matter degradation (e.g. Syntrophobacterales, Bacteroidales and Desulfatiglandales), whereas restored marshes showed greater representation of Desulfobacterales, Desulfobulbales and Chromatiales. In vegetated habitats, microbial communities also differed between low- and mid-marsh elevations, with low marshes enriched in Syntrophobacterales and Desulfobulbales and mid marshes characterised by Ignavibacteriales and Defluviicoccales. Despite these taxonomic differences, predicted carbon-cycling pathways were remarkably similar across restoration types and elevations. This suggests that key microbial functions can recover even when community composition remains distinct, indicating rapid re-establishment of microbial functional potential following restoration.
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7. Unraveling the Influence of Behavioural Ecotypes on Fish Gut Microbiome: Focus on the Atlantic cod (Gadus morhua) in Icelandic Waters.
PMID:日期:2026-07-15This study investigated the gut microbiome of Atlantic cod in northern Icelandic waters to assess how resident (coastal) and migratory (frontal) behavioural ecotypes influence gut microbial community composition, with a focus on the effects of ecological adaptation and the potential drivers of microbial shifts within this species. A total of 81 intestinal samples from coastal and frontal Atlantic cod collected in northern Iceland in December 2021 and January 2024 were analysed using 16S rRNA gene metabarcoding. Environmental datasets from the Copernicus Marine Service were used to assess the relationship between annual shifts in microbiome composition and changes in environmental conditions. Our results highlight that the Icelandic cod gut microbiome is a highly dynamic system primarily shaped by environmental shifts, such as warming trends and anthropogenic stressors. Because different behavioural ecotypes are inherently exposed to distinct environmental configurations, these distinct macro-scale exposures may indirectly translate into ecotype-specific microbial signatures that shape the differentiation between coastal and offshore habitats; the effects were particularly evident in the coastal populations, underscoring the greater vulnerability of nearshore habitats to environmental shifts and anthropogenic stressors. These findings suggest the role of the microbiome in ecological plasticity of Atlantic cod; concurrently, they reveal distinct ecotype-specific sensitivities to environmental shifts, particularly those of anthropogenic origin, providing a valuable framework that may support future marine conservation strategies.
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8. The Microbial and Chemical Terroir of Agarwood in French Guiana.
8. 法属圭亚那沉香木的微生物与化学风土PMID:日期:2026-07-15[中文摘要] 沉香是沉香属（Aquilaria）树种在受到胁迫或感染后形成的一种高价值芳香树脂木材，然而对其品质的潜在微生物驱动因素仍知之甚少，尤其是在其原生分布范围之外。本研究调查了法属圭亚那种植的沉香树（Aquilaria crassna Pierre ex Lecomte）所产沉香相关的细菌和真菌群落，并考察了其与沉香香气相关挥发性化合物的关系。利用高通量测序和全面的化学谱分析，我们在多个种植地块中表征了微生物群落组成和沉香挥发性成分谱。尽管微生物群落存在空间变异，沉香样品仍表现出以色酮衍生物和倍半萜类为主的保守化学特征，表明在圭亚那环境条件下存在稳定的化学风土。网络分析揭示了众多与关键化学类别显著相关的细菌和真菌类群，提示微生物可能通过植物-微生物相互作用或微生物代谢活动对沉香化学复杂性作出贡献，但其因果关系尚待确立。与来自东南亚和中东的商业沉香样品的比较分析显示，圭亚那沉香具有独特的化学谱，凸显了地理来源对沉香品质的影响，并支持将风土概念扩展至木质芳香产品。总体而言，本研究表明在法属圭亚那栽培的沉香树能够产出高品质沉香，并为微生物群落与沉香化学之间的相互作用提供了新的见解。这些发现为开发适应当地、基于微生物组的可持续沉香生产策略奠定了基础。
[英文摘要] Agarwood is a highly valued aromatic resinous wood formed in Aquilaria species following stress or infection, yet the putative microbial drivers of its quality remain poorly understood, particularly outside its native range. In this study, we investigated the bacterial and fungal communities associated with agarwood produced from Aquilaria crassna Pierre ex Lecomte planted in French Guiana and examined their relationships with volatile chemical compounds relevant to agarwood fragrance. Using high‑throughput sequencing and comprehensive chemical profiling, we characterized microbial community composition and agarwood volatile profiles across multiple cultivation plots. Despite spatial variability in microbial assemblages, agarwood samples exhibited a conserved chemical signature dominated by chromone derivatives and sesquiterpenoids, indicating the presence of a stable chemical terroir under Guianese environmental conditions. Network analysis revealed numerous bacterial and fungal taxa significantly associated with key chemical classes, suggesting potential microbial contributions to agarwood chemical complexity through plant-microbe interactions or microbial metabolic activity, although causality remains to be established. Comparative analyses with commercial agarwood samples from South-East Asia and the Middle East revealed a distinct chemical profile for Guianese agarwood, highlighting the influence of geographic origin on agarwood quality and supporting an extension of the terroir concept to woody aromatic products. Overall, this study demonstrates that Aquilaria trees cultivated in French Guiana can produce high‑quality agarwood and provides new insights into the interplay between microbial communities and agarwood chemistry. These findings lay the groundwork for the development of locally adapted, microbiome‑informed strategies for sustainable agarwood production.
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10. Metabarcoding Characterization of Fungal Communities in Spanish Cereals with a Special Focus on Fusarium Species.
10. 西班牙谷物中真菌群落的宏条形码表征：以镰刀菌属为重点PMID:日期:2026-07-11Cereal safety is a critical public health concern, as crops are frequently compromised by mycotoxin-producing fungi, particularly those from the genus Fusarium. Although metabarcoding is a powerful tool for characterizing these fungal communities, the universal internal transcribed spacer 2 (ITS2) marker lacks the resolution required to distinguish closely related species with distinct toxigenic profiles. The objective of this work was to accurately characterize the mycobiota and specific Fusarium community structure in Spanish cereal field samples. We propose a high-resolution metabarcoding workflow within the QIIME 2 environment to optimize Fusarium identification using the translation elongation factor 1-α (TEF1) gene. We developed a TEF1 Naive Bayes classifier trained on a curated database derived from FUSARIUM-ID v.3.0, expanded with eukaryotic sequences to prevent false-positive assignments. This approach was validated through direct comparison with ITS2 in the same samples. As expected, ITS2 significantly underestimates Fusarium diversity, whereas TEF1 enables precise species-level resolution within this genus. General mycobiota analysis performed using ITS2 revealed that fungal communities are shaped primarily by geographical location rather than host cereal species. Crucially, our approach confirmed the persistence of key toxigenic species, such as F. langsethiae and F. graminearum, and revealed broader diversity through the consistent detection of species often overlooked by traditional methods, including F. equiseti, F. acuminatum, and F. culmorum. We conclude that our metabarcoding framework reveals a high Fusarium diversity in Spanish cereal grains, and this knowledge is essential for designing targeted strategies to predict and mitigate mycotoxin contamination in these crops.