Simple, reference-independent analyses help optimize hybrid assembly of microbial community metagenomes DOI Creative Commons
Garrett J. Smith,

Theo van Alen,

Maartje A. H. J. van Kessel

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Sept. 15, 2023

Abstract Hybrid metagenomic assembly, leveraging both long- and short-read sequencing technologies, of microbial communities is becoming an increasingly accessible approach, yet its widespread application faces several challenges. High-quality references may not be available for assembly accuracy comparisons common benchmarking, certain aspects hybrid require dataset-dependent, empirically-guided optimization rather than a uniform approach. In this study, simple, reference-free characteristics – gene lengths read recruitment were analyzed as reliable proxies quality to guide optimization. These further explored in relation reference-dependent genome- gene-centric analyses that are community studies. Here, two laboratory-scale bioreactors sequenced with short long platforms, assembled commonly used software packages. Following correction polishing iterated resolve errors. Each iteration process was shown so have substantial effect on gene- genome-centric composition. Simple, characteristics, specifically changes fragmentation recruitment, throughout replicated patterns more advanced seen published comparative studies, therefore suitable metagenome save computational resources. approaches will likely remain relevant due the low costs sequencing, it imperative users equipped estimate prior downstream analyses.

Language: Английский

Unraveling the role of bacterial communities in mangrove habitats under the urban influence, using a next-generation sequencing approach DOI Creative Commons
Mayukhmita Ghose, Ashutosh Shankar Parab, Cathrine Sumathi Manohar

et al.

Journal of Sea Research, Journal Year: 2024, Volume and Issue: 198, P. 102469 - 102469

Published: Jan. 11, 2024

Mangrove ecosystems are vital coastal habitats with rich biodiversity and play a significant role in carbon sequestration, these facing mounting threats from rapid urbanization. This study delves into assessing the sediment bacterial communities urban mangrove of Campal Panaji, within Mandovi estuarine environment Goa, to understand intricate interplay between urbanization dynamics habitats. We used combined approach 16S amplicon shotgun sequencing methodologies taxonomic composition functional profiles. The community structure revealed dominance groups phylum Proteobacteria, Chloroflexi Actinobacteria at both locations. impact was evident increased abundance pathogenic class genus levels this region. core microbiome analysis showed presence Shewanella, Pseudomonas Clostridium which mostly pathogenic, anaerobic taxa Woeseia, Rheinheimera, like genera that involved organic matter cycling unclassified bacteria. Though forms reported, it is dominant also included contributed biogeochemical Functional diversity elucidated through metagenomics showcased predominance carbohydrate metabolism glycoside hydrolases degrading plant-based starch, pectin cellulosic matter. occurrence xenobiotic biodegradation pathways an indication microbes as natural means high amounts pollutants location. Comparative metagenomes similar earlier studies Ribandar, Cortalim, Zuari Goa varying pollution reiterates terrestrial influence on microbial It Panaji locations had absent other two Ribandar Coratlim location reported have comparatively lesser due anthropogenic activity distinct predominant heterotrophic remineralization reduced pathogens. Our findings highlight profound spotlight resilience adaptability microorganisms. calls for immediate action preventive measures restore their potential maintaining health amidst expanding landscapes.

Language: Английский

Citations

12
Analysis of metagenomic data DOI
Shaopeng Liu, Judith Rodríguez, Viorel Munteanu

et al.

Nature Reviews Methods Primers, Journal Year: 2025, Volume and Issue: 5(1)

Published: Jan. 23, 2025

Language: Английский

Citations

1
Comparative metagenomics reveals the metabolic flexibility of coastal prokaryotic microbiomes contributing to lignin degradation DOI Creative Commons
Qiannan Peng, Lin Lu

Biotechnology for Biofuels and Bioproducts, Journal Year: 2025, Volume and Issue: 18(1)

Published: Jan. 18, 2025

Coastal wetlands are rich in terrestrial organic carbon. Recent studies suggest that microbial consortia play a role lignin degradation coastal wetlands, where turnover rates likely underestimated. However, the metabolic potentials of these remain elusive. This greatly hinders our understanding global carbon cycle and "bottom-up" design synthetic to enhance conversion. Here, we developed two groups degrading consortia, L6 L18, through 6- 18-month situ enrichments East China Sea, respectively. Lignin by L18 was 3.6-fold higher than L6. Using read-based analysis, 16S rRNA amplicon metagenomic sequencing suggested possessed varied taxonomic compositions, yet similar functional traits. Further comparative based on assembly, revealed harbored abundant metagenome-assembled genomes (MAGs) encoded diverse unique gene clusters (LDGCs). Importantly, anaerobic MAGs were significantly enriched highlighting degradation. Furthermore, generalist taxa, which possess flexibility, increased during extended enrichment period, indicating advantage generalists adapting heterogenous resources. study advances strategies prokaryotic lays foundation for communities sustainable lignocellulose biorefining.

Language: Английский

Citations

0
Seasonal dynamics of bacterial communities in mangrove sediments of Shupaisha island, Zhejiang Province, China DOI Creative Commons
Maoqiu He, Suhua Jiang,

Xiangfu Li

et al.

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

Published: Feb. 19, 2025

Mangrove forests, found primarily in tropical and subtropical coastal regions, support diverse microbial communities that are crucial for nutrient cycling energy flow then sustain mangrove ecosystem integrity. This study investigated the seasonal dynamics of bacterial sediments Shupaisha island (Zhejiang Province, China) through amplifying high-throughput sequencing 16S rRNA gene fragments. Proteobacteria (23.59-44.40%), Actinobacteria (4.92-19.01%), Bacteroidetes (4.31-22.79%) dominated phyla with highest diversity indices winter. were more abundant during winter (13.27%) spring (14.36%), while abundance was summer, significantly correlating temperature. Significant differences community composition observed between autumn exhibited similar distribution, indicating a transitional pattern dynamics, temperature sand content being most influential factors. enhances our understanding characteristics ecosystems, potentially providing valuable insights into monitoring assessing health stability ecosystems Zhejiang Province.

Language: Английский

Citations

0
Coupling of Sulfate Reduction and Dissolved Organic Carbon Degradation Accelerated by Microplastics in Blue Carbon Ecosystems DOI
Heli Wang, Yin Zhong,

Qian Yang

et al.

Water Research, Journal Year: 2025, Volume and Issue: 279, P. 123414 - 123414

Published: Feb. 28, 2025

Language: Английский

Citations

0
Sequencing the unseen: long-read metagenomics and the microbial frontier DOI

Fatemeh Yaghoobizadeh

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown, P. 65 - 97

Published: Jan. 1, 2025

Language: Английский

Citations

0
Exploring the rich diversity and ecological roles of fungal communities in a small yet vibrant mangrove ecosystem DOI
Hawa Myovela, Donatha D. Tibuhwa, Juma Mahmud Hussein

et al.

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

Published: March 24, 2025

Language: Английский

Citations

0
Culturing the uncultured marine fungi in the omics age: Opportunities and challenges DOI
Zhifeng Zhang, Fang Liu,

Lirui Liu

et al.

Fungal Biology Reviews, Journal Year: 2024, Volume and Issue: 48, P. 100353 - 100353

Published: Jan. 4, 2024

Language: Английский

Citations

3
Living in mangroves: a syntrophic scenario unveiling a resourceful microbiome DOI Creative Commons
Marcele Laux, Luciane Prioli Ciapina, Fabíola Marques de Carvalho

et al.

BMC Microbiology, Journal Year: 2024, Volume and Issue: 24(1)

Published: June 28, 2024

Abstract Background Mangroves are complex and dynamic coastal ecosystems under frequent fluctuations in physicochemical conditions related to the tidal regime. The variation organic matter concentration, nutrients, oxygen availability, among other factors, drives microbial community composition, favoring syntrophic populations harboring a rich diverse, stress-driven metabolism. known for their carbon sequestration capability, integrated metabolic activity is essential global biogeochemical cycling. Here, we present reconstruction based on genomic functional capability flux profile between sympatric MAGs co-assembled from tropical restored mangrove. Results Eleven were assigned six Bacteria phyla, all distantly available reference genomes. showed several potential coupling points shortcuts complementary routes predicted interactions. Two scenarios drawn: heterotrophic scenario with plenty of sources an autotrophic limited or inhibitory conditions. sulfur cycle was dominant over methane major pathways identified acetate oxidation coupled sulfate reduction, acetogenesis carbohydrate catabolism, ethanol production fixation. Interestingly, gene sets similar those described wastewater effluent treatment processes identified. Conclusion mangrove reflected flexibility required survive fluctuating environments as microhabitats created by regime sediments. components strongly suggest that communities could represent resourceful model biotechnological applications occur naturally environment.

Language: Английский

Citations

3
Fungi promote cross-domain interactions even in deep anoxic mangrove sediments DOI Creative Commons
Ming Sheng Ng,

Nathaniel Soon,

Min Yi Chin

et al.

Environmental Microbiome, Journal Year: 2025, Volume and Issue: 20(1)

Published: March 25, 2025

Abstract Background Microbial communities in mangrove sediments play vital ecological roles that underpin the functioning of overall ecosystem. Fungal communities, particular, are known to crucial across sediment systems, yet their sediments, especially deeper layers, remain poorly understood without a comprehensive inter-domain characterization. To better understand fungal horizons, 10 cores extending down depth 1 m were taken three sites characterise archaeal, bacterial, and at cm intervals. Results We demonstrate has distinct effects on microbial communities. While community compositions similar depths, bacterial archaeal stratified into surface (10–30 cm), subsurface (40–60 deep (70–100 cm). Co-occurrence networks then constructed investigate fungi these where consistently identified as keystone taxa maintaining network topology, with co-domain interactions constituting more than half all interactions. Even deepest layer, nodes still retained high betweenness centralities, acting hubs potentially augment for Conclusions Overall, our results emphasise important role mediating depths even deep, anoxic highlight importance cross-domain integral holistic understanding microbiome.

Language: Английский

Citations

0