Long-term cultivation of grass-legume mixtures changed the assembly process of the microbial community and increased microbial community stability DOI Creative Commons

Huilin Yan,

Xin Jin, Xueli Zhou

et al.

ISME Communications, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 12, 2024

Grass-legume mixtures are a common cultivation system on the Qinghai-Tibet Plateau, where interactions between rhizosphere microorganisms and crops under long-term complex dynamic. Investigating dynamic changes in microbial community structure ecological functions is essential. This study investigated of communities Elymus nutans Griseb. cv. Aba Medicago sativa L. Beilin grass-legume mixture at 1:1 ratio >4 years Plateau. The research focused their effects plant productivity, soil health, functions. results revealed decline grass yield properties fourth year (P < .05) significant year-to-year differences bacterial α-diversity .05). Molecular network analysis showed greater stability legumes first year, with reduced robustness by year. Additionally, average niche widths fungal were narrower than fourth, indicating adaptation to evolving environmental conditions within system. transition assembly processes from stochastic deterministic suggests shift toward more structured predictable over time. In conclusion, highlight intricate interplay dynamics, ecosystem planting mixtures. Our provide new insights into biomass dynamics this

Language: Английский

Impaired denitrification of aerobic granules in response to micro/nanoplastic stress: Insights from interspecies interactions and electron transfer processes DOI
Bing Zhang,

Bowen Qi,

Wenxin Shi

et al.

Water Research, Journal Year: 2025, Volume and Issue: 279, P. 123472 - 123472

Published: March 9, 2025

Language: Английский

Citations

2
Genetic and species rearrangements in microbial consortia impact biodegradation potential DOI Creative Commons
Zaki Saati‐Santamaría, Pilar Navarro‐Gómez,

Juan A Martínez-Mancebo

et al.

The ISME Journal, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 24, 2025

Language: Английский

Citations

1
Soil fungal community and co-occurrence network patterns at different successional stages of black locust coppice stands DOI Creative Commons
Huimei Tian,

Liangzhe Li,

Yunpeng Zhu

et al.

Frontiers in Microbiology, Journal Year: 2025, Volume and Issue: 16

Published: March 18, 2025

Black locust (Robinia pseudoacacia L.) plantations transition from seedling to multi-generation coppice systems, leading declines in productivity and biodiversity. However, the structural functional reorganization of soil fungal communities during this remains poorly understood. This study aimed characterize community dynamics across successional stages black stands assess their implications for health ecosystem resilience. Soil three (first-generation forest, first- second-generation forests) were analyzed over one year using ITS high-throughput sequencing. We evaluated diversity, guild composition, co-occurrence networks, integrating statistical analyses (PERMANOVA, ANOSIM, FUNGuild) network theory seasonal shifts. Fungal richness diversity remained stable stand types seasons. these factors dramatically altered structure. Shifts composition observed stands: Ascomycota dominance decreased (72.9 57.9%), while Basidiomycota increased (6.5 11.6%). Significant changes relative abundance certain guilds by both conversion variation (p < 0.05). overall was only significantly affected variation, rather than > Furthermore, saprotrophic fungi dominated autumn/winter (66.49-76.01%), whereas symbiotic peaked spring (up 7.27%). As forests seeding stands, percentage negative edges, average degree, modularity networks all gradually decreased. Those suggested that connectivity between species, formed less organized structure, homogeneity function among microbial communities, reduced ecological functionality, resistance environmental changes. Seasonal temperature fluctuations further modulated complexity, with summer samples showing heightened edge density but cooperation. Our findings suggest can shift structure assembly, favoring reducing stability. These shifts signal progressive nutrient depletion homogenization, potentially compromising highlight fungi's role cycling, saprotrophs driving litter decomposition colder months. understanding forest management practices must prioritise preservation early stages. is vital support diverse complex ensure stability, functionality communities. Restoration efforts focus on promoting resilience through targeted amendments habitat diversification enhance stability functionality.

Language: Английский

Citations

1
Characteristics of microbial carbon pump in the sediment of kelp aquaculture zone and its contribution to recalcitrant dissolved organic carbon turnover: insights into metabolic patterns and ecological functions DOI

Jun‐Yang Ma,

Jihua Liu,

Cheng-Zhuang Chen

et al.

Environmental Research, Journal Year: 2025, Volume and Issue: unknown, P. 121559 - 121559

Published: April 1, 2025

Language: Английский

Citations

1
iNAP 2.0: Harnessing metabolic complementarity in microbial network analysis DOI Creative Commons
Xi Peng, Kai Feng, Xingsheng Yang

et al.

iMeta, Journal Year: 2024, Volume and Issue: 3(5)

Published: Sept. 23, 2024

Abstract With the widespread adoption of metagenomic sequencing, new perspectives have emerged for studying microbial ecological networks, yielding metabolic evidence interspecies interactions that traditional co‐occurrence networks cannot infer. This protocol introduces integrated Network Analysis Pipeline 2.0 (iNAP 2.0), which features an innovative complementarity network studies from metagenomics sequencing data. iNAP sets up a four‐module process interaction analysis, namely: (I) Prepare genome‐scale models; (II) Infer pairwise (III) Construct networks; and (IV) Analyze networks. Starting metagenome‐assembled or complete genomes, offers variety methods to quantify potential trends between models, including PhyloMint pipeline based on phylogenetic distance‐adjusted complementarity, SMETANA (species analysis) approach cross‐feeding substrate exchange prediction, distance calculation parsimonious flux balance analysis (pFBA). Notably, integrates random matrix theory (RMT) find suitable threshold construction. Finally, can proceed using topological feature such as hub node determination. In addition, key is identification potentially transferable metabolites species, presented intermediate nodes connect in network. To illustrate these features, we use set genomes example comprehensively document usage tools. available at https://inap.denglab.org.cn all users register free.

Language: Английский

Citations

6
Metabolic synergy and complementarity in the Ips typographus holobiont DOI Creative Commons
Zaki Saati‐Santamaría, Martin Kostovčík, Tereza Veselská

et al.

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 5, 2025

Abstract Microbial symbiosis plays a central role in shaping ecological and evolutionary processes, driving the adaptation of host organisms to challenging environments. However, mechanisms underlying functional integration metabolic cooperation within holobionts remain poorly understood. Current research often emphasizes taxonomic composition microbiomes, but interactions that sustain these associations are less explored, especially nutrient-poor ecosystems. This study addresses this knowledge gap by investigating interdependencies gut microbiome European spruce bark beetle (Ips typographus, ESBB). Using meta-transcriptomic analyses, we reveal critical contributions bacterial fungal symbionts facilitating survival. Our findings show microbial partners compensate for deficiencies, with cross-kingdom enabling biosynthesis essential nutrients such as amino acids vitamins. Furthermore, division labor among taxa is evident, bacteria primarily degrading plant polymers xylan pectin, fungi specializing glucan degradation. Functional redundancy key pathways suggests an adaptive mechanism ensure nutrient availability under fluctuating community composition. In addition, identify previously unappreciated pathway nitrogen acquisition via oxidation inorganic nitrogen. highlight importance their success symbiotic associations. results provide framework exploring cycling resource use.

Language: Английский

Citations

0
Stable isotope probing and oligotyping reveal the impact of organophosphorus pesticides on the carbon fixation related bacterioplankton lineage DOI
En Xie, Ziwei Chen, Xu Zhang

et al.

Journal of Hazardous Materials, Journal Year: 2025, Volume and Issue: 492, P. 138159 - 138159

Published: April 4, 2025

Language: Английский

Citations

0
Changes in the community composition and function of the rhizosphere microbiome in tobacco plants with Fusarium root rot DOI Creative Commons
Min Yang, Yongzhan Cai, Tao Bai

et al.

Frontiers in Microbiology, Journal Year: 2025, Volume and Issue: 16

Published: April 9, 2025

Introduction Tobacco root rot caused by Fusarium spp. is a soil-borne vascular disease that severely affects tobacco production worldwide. To date, the community composition and functional shifts of rhizosphere microbiome in plants infected with remain poorly understood. Methods In this study, we analyzed differences compositions functions bacterial fungal communities endosphere healthy using amplicon sequencing metagenomic sequencing. Results discussion Our results showed disrupted stability bacteria–fungi interkingdom networks reduced network complexity. Compared to plants, Chao1 index soil diseased increased 4.09% ( P &lt; 0.05), while Shannon indices decreased 13.87 8.17%, respectively 0.05). tissues 17.71–27.05% Additionally, observed microbial shifted toward pathological combination, significant increase relative abundance harmful microbes such as Alternaria, , Filobasidium (89.46–921.29%) notable decrease beneficial Lysobacter, Streptomyces, Mortierella Penicillium (48.48–81.56%). Metagenomic analysis further revealed played role basic biological metabolism, energy conversion, signal transduction, N but their involved C metabolism were significantly weakened. findings provide new insights into changes interactions within microbiomes under stress pathogens, laying foundation for exploration, development, utilization resources future.

Language: Английский

Citations

0
Pre-biodrying enhanced lignin degradation to promote aromatic macromolecular humic acid formation in double-phase composting DOI

Jiefei Mo,

Changxun Zhao,

Chenxuan Fang

et al.

Waste Management, Journal Year: 2025, Volume and Issue: 202, P. 114851 - 114851

Published: April 29, 2025

Language: Английский

Citations

0
ggClusterNet 2: An R package for microbial co‐occurrence networks and associated indicator correlation patterns DOI Creative Commons
Tao Wen, Yongxin Liu, Lanlan Liu

et al.

iMeta, Journal Year: 2025, Volume and Issue: unknown

Published: April 25, 2025

Abstract Since its initial release in 2022, ggClusterNet has become a vital tool for microbiome research, enabling microbial co‐occurrence network analysis and visualization over 300 studies. To address emerging challenges, including multi‐factor experimental designs, multi‐treatment conditions, multi‐omics data, we present comprehensive upgrade with four key components: (1) A pipeline integrating computation (Pearson/Spearman/SparCC correlations), visualization, topological characterization of node properties, multi‐network comparison statistical testing, stability (robustness) analysis, module identification analysis; (2) Network mining functions multi‐factor, multi‐treatment, spatiotemporal‐scale Facet.Network() module.compare.m.ts() ; (3) Transkingdom construction using microbiota, multi‐omics, other relevant diverse layouts such as MatCorPlot2() cor_link3() (4) corBionetwork.st() algorithms tailored complex exploration, model_maptree2() , model_Gephi.3() cir.squ() . The updates 2 enable researchers to explore interactions, offering robust, efficient, user‐friendly, reproducible, visually versatile networks indicator correlation patterns. R package is open‐source available on GitHub ( https://github.com/taowenmicro/ggClusterNet ).

Language: Английский

Citations

0