Biology subjects

Nguyen-Dinh, T.

Publications and source records attributed to Nguyen-Dinh, T..

3 recordsLinked to original sources

bioRxiv2025

Chemosynthesis enables microbial communities to flourish in a marine cave ecosystem

Chemosynthesis, an ancient metabolism that uses chemical compounds for energy and biomass generation, occurs across the ocean. Although chemosynthesis typically plays a subsidiary role to photosynthesis in the euphotic ocean, it is unclear whether it plays a more important role in aphotic habitats within this zone. Here, we compared the composition, function, and activity of sedimentary microorganisms within a marine cave at mesophotic depth, across a transect from the entrance to the interior. Microbes thrived throughout this ecosystem, with interior communities having higher diversity than those at the entrance. Analysis of 132 species-level bacterial, archaeal, and eukaryotic metagenome-assembled genomes revealed niche partitioning of habitat generalists distributed along the cave, alongside specialists enriched across its entrance and interior environments. Photosynthetic microbes and photosystem genes declined in the inner cave, concomitant with enrichment of chemosynthetic lineages capable of using inorganic compounds such as ammonium, sulfide, carbon monoxide, and hydrogen. Biogeochemical assays confirmed that the cave communities consume these compounds and fix carbon dioxide through chemosynthesis, with inner communities mediating higher cellular rates. Together, these findings suggest that the persistent darkness and low hydrodynamic disruption in marine cave sediments create conditions for metabolically diverse communities to thrive, sustained by recycling of inorganic compounds, as well as endogenous and lateral organic matter inputs. Thus, chemosynthesis can sustain rich microbial ecosystems even within the traditionally photosynthetically dominated euphotic zone.

ecology↗

bioRxiv2025

Chemosynthesis enhances carbon fixation in an active microbialite ecosystem

Microbialites--carbonate structures formed under the influence of microbial action-- are the earliest macroscopic evidence of life. For three billion years, the microbial mat communities responsible for these structures fundamentally shaped Earths biogeochemical cycles. In photosynthetic microbial communities, light energy ultimately drives primary production and the ensuing cascade of daisy-chained metabolisms. However, reduced compounds such as trace gases and those released as metabolic byproducts in deeper, anoxic regions of the mat, could also fuel chemosynthetic processes. Here, we investigated the intricate metabolic synergies that sustain microbialite community nutrient webs. We recovered 331 genomes spanning 40 bacterial and archaeal phyla, revealing a staggering diversity fuelled by the biogeochemistry of these ecosystems. While phototrophy is an important metabolism encoded by 17% of the genomes, over half encode enzymes to harness energy from reduced compounds and 12% co-encode carbon fixation pathways, using sulfide and hydrogen as major electron donors. Consistent with these genomic predictions, we experimentally demonstrated that microbialite communities oxidise ferrous iron, ammonia, sulfide and gas substrates aerobically and anaerobically. Furthermore, carbon isotopic assays revealed that diverse chemosynthetic pathways contribute significantly to carbon fixation and ecosystem organic matter production alongside photosynthesis. Chemosynthesis in microbialite communities represents a complex interplay of metabolic synergies and continuous nutrient cycling, which decouples community carbon fixation from the diurnal cycle. As a result, this process mitigates the loss of organic carbon from respiration, enhancing the net productivity of these highly efficient ecosystems. SignificanceMicrobialite ecosystems are among the most ancient on Earth, having dominated the biosphere for over three billion years and persisting into the present. They serve as critical models for studying past and present Earth-biosphere interactions. In this study, we challenge the paradigm that photosynthesis is the main driver of microbialite primary productivity, emphasizing the fundamental role of chemosynthesis in the global element cycle both in modern extreme environments and throughout Earths history. Altogether, our findings provide novel insight into these unique microbial ecosystems, which may have functioned as hotspots for metabolic innovation over geological time.

microbiology↗

bioRxiv2024

Hydrogen-dependent dissimilatory nitrate reduction to ammonium enables growth of Campylobacterota isolates

Dissimilatory nitrate reduction to ammonium (DNRA) is a key process in global nitrogen cycling, supporting the energy conservation of diverse microbes. For a long time, DNRA has been thought to primarily depend on organic electron donors, and thus to be governed by carbon-to-nitrogen (C:N) ratios. However, recent studies suggest that inorganic electron donors, such as sulfur compounds and iron, may also facilitate DNRA. The coupling of DNRA with molecular hydrogen (H2) oxidation is theoretically feasible, but largely unexplored microbial process. Here, we report the isolation of two Campylobacterota strains, Aliarcobacter butzleri hDNRA1 and Sulfurospirillum sp. hDNRA2, that grow by using H2 as an electron donor for DNRA. In both batch and continuous cultures, DNRA sensu stricto, i.e., NO2--to-NH + reduction, depended on the presence of H2 and was stoichiometric with H2 oxidation. The electrons for NO - reduction were clearly derived from H, and hydrogenotrophic DNRA was largely unaffected by the ratio of either carbon or electron donor to NO -/NO -. Genomic and transcriptomic analyses indicate that group 1b [NiFe]-hydrogenase and cytochrome c552 nitrite reductase are the key enzymes catalyzing hydrogenotrophic DNRA. These findings reveal novel physiological mechanisms enabling anaerobic bacterial growth, challenge the traditional C:N ratio paradigm, and uncover new biogeochemical processes and mediators controlling the global nitrogen and hydrogen cycles.

microbiology↗