Mapping the global ocean genome DOI

Published: Feb. 21, 2024

The global ocean genome (the pool of genes in marine organisms and the functional information they encode) is a major, untapped resource for science society with growing range biotechnology applications sectors such as biomedicine, energy, food. Shotgun sequencing metagenomics can now be used to catalog diversity microbial life explore its potential, but has been limited by sample coverage, access suitable platforms, computational capacity. Here we provide novel synthesis based on analysis 2,102 sampled metagenomes, gene assembly annotation via KAUST Metagenome Analysis Platform (KMAP) Global Ocean Gene Catalog 1.0 containing 308.6 million clusters. Taxonomically, report distribution across tree different basins depth zone biomes. Functionally, map relationship protein families biogeochemical processes, including major metabolic pathways that process three elements play fundamental roles cycles are relevant climate change. These data extend our understanding complex, dynamic nature microbiome capabilities. Further research critical importance both unlock potential understand predict effects human-induced changes, pollution hypothesis-driven should target under-sampled deep sea benthic communities using enhanced metagenomic methods, better ecosystem functioning. Investment necessary capacity essential, intellectual property frameworks.

Language: Английский

Immunomodulatory Compounds from the Sea: From the Origins to a Modern Marine Pharmacopoeia DOI Creative Commons
Edoardo Andrea Cutolo, Rosanna Campitiello, Roberto Caferri

et al.

Marine Drugs, Journal Year: 2024, Volume and Issue: 22(7), P. 304 - 304

Published: June 28, 2024

From sea shores to the abysses of deep ocean, marine ecosystems have provided humanity with valuable medicinal resources. The use organisms is discussed in ancient pharmacopoeias different times and geographic regions still deeply rooted traditional medicine. Thanks present-day, large-scale bioprospecting rigorous screening for bioactive metabolites, ocean coming back as an untapped resource natural compounds therapeutic potential. This renewed interest drugs propelled by a burgeoning research field investigating molecular mechanisms which newly identified intervene pathophysiology human diseases. Of great clinical relevance are molecules endowed anti-inflammatory immunomodulatory properties emerging applications management chronic inflammatory disorders, autoimmune diseases, cancer. Here, we review historical development pharmacology Eastern Western worlds describe status drug discovery. Finally, discuss importance conducting sustainable exploitation resources through biotechnology.

Language: Английский

Citations

4
Biobanking marine biodiversity in the Arctic DOI Creative Commons

Darya Chernikhova,

Charla J. Basran

Frontiers in Marine Science, Journal Year: 2025, Volume and Issue: 11

Published: Feb. 17, 2025

Biorepositories, or biobanks, are vital to marine science. Their collections safeguard biological knowledge, enable follow-up studies and reproducibility confirmations, help extend ecological baselines. Biorepository networks data portals aggregate catalogs facilitate open material exchange. Such integrations enrich contextual support holistic ecosystem-based research management. In the Arctic, where researchers face vast scales, rapidly changing ecosystems, limited resampling opportunities, biobanking builds capacities. However, polar biodiversity remains underrepresented in collections. Heterogeneous methodologies documentation practices hinder integrations. And science faces high institutional cultural barriers. Here, we explore potential of amplify impact individual studies. We address gaps standardization vouchering suggest improvements funding publishing models incentivize collaboration. bring together calls for advancements from diverse perspectives provide examples expeditions, databases, specimen collections, standards. The general analysis is illustrated with two case studies, showcasing range field: inclusion citizen observations cetacean monitoring, preservation specimens environmental microbiome former, strategies harmonizing collection global databases. latter, propose cooperative field intact living (complex microbial community) cryopreservation. Our perspective frames as a strategy, essential accelerating under current climate change-related pressures. advocate international investment precautionary approach academic conservation stewardship Arctic heritage.

Language: Английский

Citations

0
Association of Microbial Networks with the Coastal Seafloor Macrofauna Ecological State DOI Creative Commons

Tonje Nilsen,

Ragnhild Pettersen, Nigel Keeley

et al.

Environmental Science & Technology, Journal Year: 2025, Volume and Issue: unknown

Published: April 11, 2025

Recent evidence suggests that there is a major switch in coastal seafloor microbial ecology already at mildly deteriorated macrofaunal state. This knowledge of critical value the management and conservation seafloor. We therefore aimed to determine relationships between microbiota macrofauna on regional scale. compared prokaryote, macrofauna, chemical, geographical data from 1546 samples, which varied their exposure aquaculture activities along Norwegian Icelandic coasts. found samples contained either network centralized by sulfur oxidizer (42.4% n = 656) or an archaeal ammonium (44.0% 681). Very few neither (9.8% 151) both (3.8% 58). Samples with had 10-fold higher risk loss (odds ratios, 95% CI: 9.5 15.6), while those lower (95% 0.068 0.11). The was negatively correlated distance sites (Spearman rho -0.42, p < 0.01) present all (n 274). absent positively 0.67, 0.01). Based 356 high-quality metagenome-assembled genomes (MAGs), we bicarbonate-dependent carbon fixation low-affinity oxygen respiration were associated network, retention, metabolism, high-affinity respiration. In conclusion, our findings highlight roles networks oxidizers mild deterioration, should be included as essential part surveillance.

Language: Английский

Citations

0
Bacterial Communities in the East African Coastal Waters of the Indian Ocean DOI Creative Commons
Ola A. Olapade

African Journal of Ecology, Journal Year: 2025, Volume and Issue: 63(3)

Published: April 1, 2025

ABSTRACT Presently, very sparse information exists about the occurrences and diversity of microbes in western Indian Ocean (WIO) relative to other areas ocean. In this study, high‐throughput sequencing 16S rRNA genes metagenomic approaches were utilised examine microbial assemblages Kenya Tanzania. Results from 24 locations showed that Proteobacterial members made up majority bacterial assemblages. Other dominant phyla Bacteroidetes (9%–10%), Firmicutes (1.4%–8%), Actinobacteria (4%–6%) Acidobacter (3.4%–3.6%). Combinations (alpha beta) as well Pearson correlation analyses clustered together differed those Tanzania because covariation with various environmental factors, such temperature salinity.

Language: Английский

Citations

0
The 2030 Declaration on Scientific Plant and Fungal Collecting DOI Creative Commons
Alexandre Antonelli, Jordan K. Teisher, Rhian J. Smith

et al.

Plants People Planet, Journal Year: 2024, Volume and Issue: 7(1), P. 11 - 22

Published: Sept. 30, 2024

Societal Impact Statement Biological samples and their associated information are an essential resource used by scientists, governments, policymakers, practitioners communities to ensure that biodiversity can be appropriately protected sustainably used. Yet, considering the enormous task of documenting vast numbers as‐yet‐unknown plant fungal species, greater international coordination for biological collecting recording is necessary, built on equitable practices standards. Here, we propose five commitments accelerate enhance scientific knowledge diversity, while increasing collaboration, benefit sharing efficiency. Summary Almost all life depends plants fungi, making diversity distribution—primarily derived from collections—fundamental national conservation, restoration sustainable use commitments. However, it estimated some 15% species over 90% have not yet been scientifically described, hampering our ability assess demonstrate impact efforts halt loss. In addition, organisations researchers around world lack a concerted strategy complementarity avoiding overlap in botanical mycological research, particularly relation collection specimens. We here present 2030 Declaration Scientific Plant Fungal Collecting, summarising commitment towards such necessary strategy. Its components were identified discussions during after series four workshops plenary at 2023 State World's Plants Fungi symposium convened Royal Botanic Gardens, Kew, then consolidated into form authors. The was subsequently opened up endorsement signatories. Collectively, agree set cataloguing world's flora funga, designed maximise efficiency, facilitate exchange promote collaborations: (1) evidence‐based strategies; (2) strengthen local capacity; (3) collaborate across taxa disciplines; (4) collect future; (5) share benefits. This first step increased global regional efforts.

Language: Английский

Citations

3
Functional Genomics of a Collection of Gammaproteobacteria Isolated from Antarctica DOI Creative Commons

Michele Giovannini,

Walter Vieri,

Emanuele Bosi

et al.

Marine Drugs, Journal Year: 2024, Volume and Issue: 22(6), P. 238 - 238

Published: May 23, 2024

Antarctica, one of the most extreme environments on Earth, hosts diverse microbial communities. These microbes have evolved and adapted to survive in these hostile conditions, but knowledge molecular mechanisms underlying this process remains limited. The Italian Collection Antarctic Bacteria (Collezione Italiana Batteri Antartici (CIBAN)), managed by University Messina, represents a valuable repository cold-adapted bacterial strains isolated from various environments. In study, we sequenced analyzed genomes 58 marine Gammaproteobacteria CIBAN collection, which were during expeditions 1990 2005. By employing genome-scale metrics, taxonomically characterized assigned them four distinct genera: Pseudomonas, Pseudoalteromonas, Shewanella, Psychrobacter. Genome annotation revealed previously untapped functional potential, including secondary metabolite biosynthetic gene clusters antibiotic resistance genes. Phylogenomic analyses provided evolutionary insights, while assessment cold-shock protein presence shed light adaptation mechanisms. Our study emphasizes significance as resource for understanding life its biotechnological potential. genomic data unveil new horizons insight into existence Antarctica.

Language: Английский

Citations

2
Metagenomic Analysis of Microbial Diversity in the Moroccan Coastal Water of the Gibraltar Strait DOI Open Access

Manal Chrairi,

Saïd Barrijal,

Antonio Castellano‐Hinojosa

et al.

Water, Journal Year: 2024, Volume and Issue: 16(22), P. 3202 - 3202

Published: Nov. 8, 2024

Coastal waters are known for higher productivity and organic matter levels, which support a high diversity abundance of microorganisms compared to some aquatic environments. The characterization marine microbiomes can provide valuable information evaluating the sustainability coastal that increasingly subjected environmental human impacts. Our study is first metagenomic realized on Moroccan Mediterranean seawater. We analyzed described Gibraltar Detroit microbiome taxonomic functional profiling using MG-RAST software. Shotgun sequencing revealed predominance bacterial taxa, particularly Proteobacteria (57.29%) Bacteroidetes (27.06%) phyla, alongside notable populations eukaryotes, viruses, archaea. Alphaproteobacteria Gammaproteobacteria emerged as dominant classes, while Flavobacteria represented significant portion Bacteroidetes. Functional microbial community highlighted wide array metabolic pathways, emphasizing genes related carbohydrate metabolism, amino acid synthesis, protein processing. exhibited essential biogeochemical activities, in nitrogen, sulfur, carbon cycles, with pathways including denitrification, thiosulfate oxidation, fixation. This underlines microbiome’s role sustaining ecosystem health through nutrient cycling degradation. findings offer crucial baseline understanding structure resilience ecosystems, implications assessing future anthropogenic impacts these dynamics.

Language: Английский

Citations

1
Largest genetic database of marine microbes could aid drug discovery DOI
Carissa Wong

Nature, Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 16, 2024

Language: Английский

Citations

0
Understanding the ocean metagenome DOI Creative Commons
Enric Sala

Frontiers in Science, Journal Year: 2024, Volume and Issue: 1

Published: Jan. 16, 2024

Keywords: ocean, metagenome, microbial diversity, bacteria, archaea, viruses, functional metagenomics

Language: Английский

Citations

0
New insights and research prospects from the ocean microbiome DOI Creative Commons
Andreas Teske

Frontiers in Science, Journal Year: 2024, Volume and Issue: 1

Published: Jan. 16, 2024

Keywords: shotgun metagenomics, microbes, ocean gene catalog, biodiversity, domains, functional genomics, biogeochemical cycling

Language: Английский

Citations

0