Diverse quorum sensing systems regulate microbial communication and biogeochemical processes in deep-sea cold seeps DOI Creative Commons

Jiaxue Peng,

Xinyue Liu,

Jieni Wang

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 16, 2024

Abstract Quorum sensing is a fundamental chemical communication mechanism that enables microorganisms to coordinate behavior and adapt environmental conditions. In deep-sea cold seep ecosystems, where diverse microbial communities thrive, quorum likely key driving interactions. However, the distribution, mechanisms, ecological roles of in seeps remain poorly understood. To address this, we analyzed 173 metagenomes, 33 metatranscriptomes, 18 metabolomes from 17 global sites. We identified 299,355 genes non-redundant gene catalog, representing 34 types across six systems, with distribution patterns influenced by sediment depth type. These were present 3,576 metagenome-assembled genomes 12 archaeal 108 bacterial phyla, revealing complex network intraspecies interspecies communication. Microbial groups involved metabolic processes, such as sulfate-reducing bacteria, anaerobic methanotrophic archaea, diazotrophs organohalide reducers, extensively regulated sensing, influencing biogeochemical cycles carbon, nitrogen, sulfur. Phylogenetic analysis protein domain identification highlighted functional sensing-related proteins (e.g., PDEs, CahR, RpfC/G LuxR) modulating behaviors, motility chemotaxis. Heterologous expression metabolomic profiling further confirmed activity representative LuxI-R pairs inhibitors sediments. Overall, these findings highlight complexity significance interactions, adaptation, cycling within advancing our understanding deep biosphere.

Language: Английский

Mapping the metagenomic diversity of the multi-kingdom glacier-fed stream microbiome DOI
Grégoire Michoud, Hannes Peter, Susheel Bhanu Busi

et al.

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

Published: Jan. 2, 2025

Language: Английский

Citations

2
Integrating network and in-silico simulation insights into the ecological interactions shaped by carbon sources in partial denitrification and anammox system DOI
Depeng Wang, Jialei Li, Yujie Zhang

et al.

Water Research, Journal Year: 2025, Volume and Issue: 276, P. 123246 - 123246

Published: Feb. 5, 2025

Language: Английский

Citations

1
A comprehensive catalog encompassing 1376 species-level genomes reveals the core community and functional diversity of anammox microbiota DOI
Depeng Wang, Yabing Meng, Li‐Nan Huang

et al.

Water Research, Journal Year: 2024, Volume and Issue: 266, P. 122356 - 122356

Published: Aug. 29, 2024

Language: Английский

Citations

8
Comprehensive blueprint of Salmonella genomic plasticity identifies hotspots for pathogenicity genes DOI Creative Commons
Simran Krishnakant Kushwaha, Yi Wu, Hugo Leonardo Ávila

et al.

PLoS Biology, Journal Year: 2024, Volume and Issue: 22(8), P. e3002746 - e3002746

Published: Aug. 7, 2024

Understanding the dynamic evolution of Salmonella is vital for effective bacterial infection management. This study explores role flexible genome, organised in regions genomic plasticity (RGP), shaping pathogenicity lineages. Through comprehensive analysis 12,244 spp. genomes covering 2 species, 6 subspecies, and 46 serovars, we uncover distinct integration patterns pathogenicity-related gene clusters into RGP, challenging traditional views distribution. These RGP exhibit preferences specific spots, presence or absence such spots across lineages profoundly shapes strain pathogenicity. are guided by conserved flanking genes surrounding implicating their involvement regulatory networks functional synergies with integrated clusters. Additionally, emphasise multifaceted contributions plasmids prophages to diverse Overall, this provides a blueprint potential . unique insight identifies nonpathogenic that hold harbouring genes, providing foundation predicting future adaptations developing targeted strategies against emerging human pathogenic strains.

Language: Английский

Citations

7
Black Carbon Impacts on Paraburkholderia xenovorans Strain LB400 Cell Enrichment and Activity: Implications toward Lower-Chlorinated Polychlorinated Biphenyls Biodegradation Potential DOI Creative Commons
Qin Dong, Gregory H. LeFevre, Timothy E. Mattes

et al.

Environmental Science & Technology, Journal Year: 2024, Volume and Issue: 58(8), P. 3895 - 3907

Published: Feb. 15, 2024

Volatilization of lower-chlorinated polychlorinated biphenyls (LC-PCBs) from sediment poses health threats to nearby communities and ecosystems. Biodegradation combined with black carbon (BC) materials is an emerging bioaugmentation approach remove PCBs sediment, but development aerobic biofilms on BC for long-term, sustained LC-PCBs remediation poorly understood. This work aimed characterize the cell enrichment activity biphenyl- benzoate-grown Paraburkholderia xenovorans strain LB400 various BCs. Biphenyl dioxygenase gene (bphA) abundance four types demonstrated corn kernel biochar hosted at least 4 orders magnitude more attached cells per gram than other feedstocks, microscopic imaging revealed live fraction was >1.5× GAC. characteristics (i.e., sorption potential, pore size, pH) appear contribute attachment differences. Reverse transcription qPCR indicated that feedstocks significantly influenced bphA expression in cells. The transcript-per-gene ratio >10-fold suspended cells, confirmed by transcriptomics. RNA-seq also significant upregulation biphenyl benzoate degradation pathways as well revealing biofilm formation potential/cell–cell communication pathways. These novel findings demonstrate PCB-degrading could be tuned adjusting feedstocks/attributes improve biodegradation potential.

Language: Английский

Citations

5
Bacterial homologs of innate eukaryotic antiviral defenses with anti-phage activity highlight shared evolutionary roots of viral defenses DOI
Daan F. van den Berg, Ana Rita Costa, Jelger Q. Esser

et al.

Cell Host & Microbe, Journal Year: 2024, Volume and Issue: 32(8), P. 1427 - 1443.e8

Published: Aug. 1, 2024

Language: Английский

Citations

5
Quorum sensing bacteria improve microbial networks stability and complexity in wastewater treatment plants DOI Creative Commons
Qiuju Liu,

Deyuan Dong,

Ying Jin

et al.

Environment International, Journal Year: 2024, Volume and Issue: 187, P. 108659 - 108659

Published: April 24, 2024

Quorum-sensing bacteria (QSB) are crucial factors for microbial communication, yet their ecological role in wastewater treatment plants (WWTPs) remains unclear. Here, we developed a method to identify QSB by comparing 16S rRNA gene sequences. 388 activated sludge samples collected from 130 WWTPs across China primarily were identified as rare taxa and conditionally taxa. A co-occurrence network shared all communities revealed that exhibited higher average clustering coefficient (0.46) than non-QSB (0.15). Individual networks demonstrated quorum sensing microbiomes positively correlated with robustness complexity, including link density. We confirmed keystones nodes have positive impact on complexity influencing modularity through structural equation model. Meanwhile, directly contributed maintaining (r = 0.29, P < 0.05). Hence, play an important promoting stability. Furthermore, associated the functional composition of 0.33, 0.01), especially denitrification capacity 0.45, 0.001). Overall, elucidated significance provided support QS-based regulation communities.

Language: Английский

Citations

4
Role of Leachate Characteristics on Carbon dots/TiO2 Photocatalytic and Bactericidal Inactivation Mechanism DOI
Qian Wang, Tong Wang, Huan Li

et al.

Journal of environmental chemical engineering, Journal Year: 2025, Volume and Issue: unknown, P. 116022 - 116022

Published: Feb. 1, 2025

Language: Английский

Citations

0
Site-specific incubations reveal biofilm diversity and functional adaptations in deep, ancient desert aquifers DOI Creative Commons
Betzabé Atencio, Stas Malavin, Maxim Rubin‐Blum

et al.

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

Published: March 21, 2025

Deep pristine aquifers are ecological hotspots with diverse microbial life, where microorganisms exist either attached (sessile) to solid substrates or suspended in groundwater (planktonic). Characterizing the communities is of paramount importance, especially context biofouling. However, obtaining samples microbes that thrive under natural (undisturbed) conditions challenging. Our study addresses this by retrieving sessile on-site. We installed columns filled site-specific rock cuttings at wellhead, allowing fresh flow continuously for approximately 60 days. hypothesized would differ structurally from planktonic due aquifer’s lithological and mineralogical composition. This involved an exploratory examination different distinct mineralogies, including quartzitic sandstone, calcareous, chert, highly heterogeneous (clastic) Israel’s Negev Desert. Metagenomic analysis revealed both shared among forms various environments, likely shaped aquifers’ physical, lithological, properties. A wealth carbon-fixation pathways energy-conservation strategies microbiome provide evidence potential productivity these biofilms. identified widespread genetic biofilm formation (e.g., via pili, flagella, extracellular polymeric substance production) interactome quorum-sensing genes). assessment functions provides a genomic framework management biofouling treatment.

Language: Английский

Citations

0
Anaerobic Acidogenesis Improvement and Fermentation-Type Regulation by Quorum Sensing DOI
Shunan Zhao, Ge Song, Suo Liu

et al.

ACS ES&T Engineering, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 11, 2024

Language: Английский

Citations

3