Seasonal Dynamics of Soil Microbiome in Response to Dry-Wet Alternation along the Jinsha River Dry-hot Valley DOI Creative Commons
Hao Jiang, Xiaoqing Chen, Yongping Li

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: July 24, 2024

Abstract Background Soil microorganisms play a key role in nutrient cycling, carbon sequestration, and other important ecosystem processes, yet their response to seasonal dry-wet alternation remains poorly understood. Here, we collected 120 soil samples from dry-hot valleys (DHVs, ~1100 m a.s.l.), transition (~2000 a.s.l.) alpine zones (~3000 along the Jinsha River southwest China during both wet dry seasons. Our aims were investigate bacterial microbiome across these zones, with specific focus on difference between Results Despite variations, communities DHVs exhibit resilience, maintaining consistent community richness, diversity, coverage. This suggests that microbes inhabiting have evolved adaptive mechanisms withstand extreme hot conditions. In addition, observed season-specific microbial clades all sampling areas, highlighting resilience adaptability environmental fluctuations. Notably, found similarities soils including phyla Actinobacteria, Chloroflexi, Proteobacteria. The neutral model respectively explained substantial proportion of variation (87.7%), (81.4%) (81%), indicating those predominantly driven by stochastic processes. results showed migration rates higher season than suggesting fewer diffusion constraints. However, this trend was reversed zones. Conclusions findings contribute better understanding how responds valley. These insights can be valuable for optimizing health enhancing particularly valleys, context climate change.

Language: Английский

Varied microbial community assembly and specialization patterns driven by early life microbiome perturbation and modulation in young ruminants DOI Creative Commons
Zhe Pan, Tao Ma, M.A. Steele

et al.

ISME Communications, Journal Year: 2024, Volume and Issue: 4(1)

Published: Jan. 1, 2024

Abstract Perturbations and modulations during early life are vital to affect gut microbiome assembly establishment. In this study, we assessed how microbial communities shifted calf diarrhea with probiotic yeast supplementation (Saccharomyces cerevisiae var. boulardii, SCB) determined the key bacterial taxa contributing shifts using a total of 393 fecal samples collected from 84 preweaned calves an 8-week trial. Our results revealed that patterns differed between healthy diarrheic at 6- trial, being stochastic-driven deterministic-driven. The two-state Markov model SCB had higher possibility shift deterministic- in calves. Furthermore, 23 21 genera were specific ecotypes SCB-responsive (SCB-fed did not exhibit diarrhea) nonresponsive occurred calves, respectively. Among these ecotypes, area under receiver operating characteristic curve Blautia Ruminococcaceae UCG 014, two unidentified family, highest predictiveness for while Prevotellaceae, Blautia, Escherichia-Shigella most predictive SCB-nonresponsive study suggests perturbations serving as deterministic factors influenced critical patterns, which sheds light on mechanisms community establishment neonatal life.

Language: Английский

Citations

6
Characteristics and assembly mechanisms of bacterial and fungal communities in soils from Chinese forests across different climatic zones DOI

Ming Sheng,

Wei Hu, Cong‐Qiang Liu

et al.

CATENA, Journal Year: 2024, Volume and Issue: 245, P. 108306 - 108306

Published: Aug. 11, 2024

Language: Английский

Citations

4
Functional microbiome assembly in food environments: addressing sustainable development challenges DOI Open Access
Yao Gu, Tingting Liu, Waleed AL‐Ansi

et al.

Comprehensive Reviews in Food Science and Food Safety, Journal Year: 2025, Volume and Issue: 24(1)

Published: Jan. 1, 2025

Abstract The global food system faces numerous challenges, creating an urgent need for sustainable reform. Functional microbiome assemblies offer transformative potential by endowing microbial foods with diverse, beneficial characteristics. These can dynamically influence specific systems, positioning them as a promising approach reshaping production. However, the current applications and types of in remain limited, lack effective screening regulatory methods. This review introduces functions practical approaches implementing systems alongside future directions enhancing their applications. Several ecological studies evaluated how to regulate functional output revealed that environmental conditions, which shape niche species survival, significantly influenced microbiomes. Building on this theoretical foundation, presents model comprising gene codes, corresponding outputs. is illustrated examples explore mechanisms assemblies. By highlighting roles outputs examining environments induce modulate functions, provides roadmap address emerging challenges sustainability.

Language: Английский

Citations

0
Resolving ecological drivers of temporal variations of β-diversity across intertidal microbiomes DOI Creative Commons
Xia Liu, Xiaofan Gong, Kai Ma

et al.

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

Published: Feb. 17, 2025

Resolving the ecological drivers mediating diversity patterns of microbial communities across space and through time is a central issue in ecology. Both regional species pools local community assembly contribute to spatial turnover biodiversity. In this study, we extended concept pool temporal, investigated seasonal dynamics intertidal microbiomes four domains/kingdoms (bacteria, archaea, fungi, protists). The results showed that variations β-diversity were primarily governed by processes rather than temporal pools. Different structured different processes, with homogeneous selection as major process for all them. Additionally, bacteria fungi critically shaped drift, protists drift dispersal. Among various factors, temperature was important shaping β-diversity. fluctuation strongly associated protists, resulting high composition. This study demonstrated dynamic β-variations microbiomes, expanding our understanding from

Language: Английский

Citations

0
Disrupting the balance: how acne duration impacts skin microbiota assembly processes DOI Creative Commons
Lang Sun,

Qingqun Wang,

Jing Huang

et al.

Microbiology Spectrum, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 24, 2025

ABSTRACT Growing interest in the impact of microbial balance on health has driven studies ecological processes shaping skin microbiota. Skin diseases, which alter skin’s local environment, can disrupt structure and interact with disease itself. However, research assembly diseased remains limited. In this study, we applied models to characterize microbiota acne patients, considering duration both pores surfaces using bacterial amplicon sequencing. Our results revealed a significant shift diversity surface patients long-term acne. Further community analyses showed transition from healthy skin. Microbial communities controls individuals short-duration were primarily by heterogeneous selection, whereas drift dominated process long-duration groups. Using Sloan neutral model, classified sequence variants (ASVs) into high-effect low-effect groups based relative abundance sample occurrence. High-effect ASVs, likely exerting greater influence, predominantly represented Cutibacterium across all acne-affected groups, while Staphylococcus became enriched among ASVs Functional profiling further demonstrated that significantly motility-related pathways. Additionally, observed reduction network complexity as increased. Overall, dynamics may offer valuable insights mechanisms underlying onset persistence. IMPORTANCE The plays critical role development, yet governing during progression remain poorly understood. Previous focused factors such severity, location, relation structure, little attention given communities. investigate influencing varying durations examined functions ecologically important non-neutral (ASVs). findings reveal deterministic increased, potentially contributing pathogenicity These contribute deeper understanding indicate targeting these or their associated serve basis for future therapeutic strategies.

Language: Английский

Citations

0
Responses of intestinal fungal community of Entomobrya proxima (Collembola: Entomobryinae) to fertilizer application DOI
Xinyue Yang, Gang Li, Weiming Xiu

et al.

Fungal Biology, Journal Year: 2025, Volume and Issue: unknown, P. 101585 - 101585

Published: April 1, 2025

Language: Английский

Citations

0
Microbial Community Response and Assembly Process of Yellow Sand Matrix in a Desert Marginal Zone Under Morchella Cultivation DOI Creative Commons

Cuicui Su,

Shengyin Zhang,

Yanfang Zhou

et al.

Microorganisms, Journal Year: 2025, Volume and Issue: 13(4), P. 921 - 921

Published: April 16, 2025

In this study, we investigated the adaptation of yellow-sand-substrate Morchella cultivation in desert fringe and its effect on soil physicochemical properties microbial communities. The qPCR high-throughput sequencing with null modeling analyzed diversity, networks, assembly under nutrient supplementation, linking changes to dynamics. results showed that yellow sand substrate can be planted area, as bags resulted a yield 691 g/m2 fruit units. Cultivation could significantly increase substrate, such organic matter (SOM), total nitrogen (TN), ammonium (NH4+−N), amount carbon (MBC/MBN). fungal community was dominated by Ascomycota, Basidiomycota, Firmicutes, Bacteroidota, Actinobacteriota. RDA analysis Ascomycota Proteobacteria were positively correlated NH4+−N, MBN, SOM, MBC, acting potassium (AK), TN, C/N. promoted positive correlation-dominant network pattern substrate. bag treatment reduced bacterial complexity while enhancing complexity, connectivity stability, accompanied significant increases Proteobacteria, Cladosporium, Thermomyces relative abundances during until original degradation. Deterministic processes communities, morel drove toward heterogeneous selection processes. study revealed economic value application potential improving sandy soil, which is great importance for practical mushrooms desert.

Language: Английский

Citations

0
Geographical patterns of mesozooplankton functional diversity in the northwestern Pacific DOI

Ruping Ge,

Hongju Chen, Tianying Chen

et al.

Progress In Oceanography, Journal Year: 2024, Volume and Issue: 221, P. 103195 - 103195

Published: Jan. 7, 2024

Language: Английский

Citations

3
Levels of microbial diversity affect the stability and function of dark fermentation bioreactors DOI Creative Commons
Marcelo Navarro-Díaz,

Valeria Aparicio-Trejo,

Idania Valdez‐Vazquez

et al.

Frontiers in Industrial Microbiology, Journal Year: 2024, Volume and Issue: 2

Published: April 25, 2024

Climate change and pollution drive the need for fossil fuel alternatives. Dark fermentation offers promise through use of microbial consortia to convert organic matter into hydrogen gas. Persisting challenges like instability low yields may stem from reduced diversity anaerobic digestion communities that serve as inoculum undergo aggressive pretreatments culturing conditions. This study explores impact loss on function, focusing biogas production stability. Two treatments, with without pretreatment, were tested 12 replicate bioreactors each, resulting in differing levels. Microbial assessed via 16S amplicon sequencing, monitoring production, volatile fatty acids, testing invasion susceptibility. The two treatments exhibited divergent assembly functional trajectories, although replicates within each treatment ultimately converged similar compositions stable levels production. Heat-treated showed a 91.5% increase but higher susceptibility compared non-treated. Non-treated unique species associations (e.g. Ethanoligenens harbinense Enterococcus olivae ), distinct commonly studied Clostridium group. These findings provide insights effects stability, elucidating differences across taxonomic stability well Moreover, identification novel bacterial groups associated suggests promising directions future research enhance control design dark fermentation.

Language: Английский

Citations

3
Quantifying functional redundancy in polysaccharide-degrading prokaryotic communities DOI Creative Commons
Dandan Li, Jianing Wang,

Yiru Jiang

et al.

Microbiome, Journal Year: 2024, Volume and Issue: 12(1)

Published: July 2, 2024

Abstract Background Functional redundancy (FR) is widely present, but there no consensus on its formation process and influencing factors. Taxonomically distinct microorganisms possessing genes for the same function in a community lead to within-community FR, assemblies of different communities playing functional roles are termed between-community FR. We proposed two formulas respectively quantify degree within between analyzed FR degrees carbohydrate degradation functions global environment samples using genetic information glycoside hydrolases (GHs) encoded by prokaryotes. Results Our results revealed that GHs each multiple taxonomically prokaryotes community, enzyme-encoding further almost any pairs. The within- between-FR primarily affected alpha beta diversities, respectively, also environmental factors (e.g., pH, temperature, salinity). prokaryotic determined deterministic Conclusions conclude stabilized characteristic. This study helps determine provides new insights into relationships biodiversity ecosystem functions.

Language: Английский

Citations

3