Semidán Robaina-Estévez

Mangroves are ecosystems located at land–sea transition zones, where they are continuously exposed to plant biomass and plastic pollution. Their soils harbor extensive microbial diversity with potential for discovering polymer-degrading enzymes. Here, we perform a microcosm experiment to examine how mangrove soil microbial communities respond to inputs of lignocellulose or polyethylene terephthalate (PET) in the presence and absence of seawater, and to explore the selection of putative PET-active enzymes (PETases) using gene- and genome-resolved metagenomics. Incubation conditions lead to a gradual increase in salinity, resulting in the enrichment of halophilic taxa, including spore-forming bacteria and archaeal species, particularly in seawater-depleted treatments. Lignocellulose input is the primary driver of soil microbial community restructuring, followed by seawater presence. In dry, lignocellulose-amended microcosms (L treatment), microbial diversity is significantly reduced, while lignocellulolytic taxa within the phyla Bacillota and Actinomycetota are enriched. Twelve potential PETases are identified in the L treatment, sharing >70% sequence similarity with known PETases, and three are predicted to be thermostable. Two putative PETases from Microbulbifer species display distinct sequence and structural features, thereby expanding the currently limited PETase sequence landscape. This study demonstrates that perturbing environmental microbiomes with plant-derived polymers represents a promising strategy for capturing novel PETases.

Mangroves are ecosystems located in land-sea transition zones, where they are continuously exposed to plant biomass inputs and plastic pollution. Their soils harbor extensive microbial diversity with potential for discovering polymer-degrading enzymes. Here, we performed a microcosm experiment to examine the responses of mangrove soil microbial communities to inputs of lignocellulose or polyethylene terephthalate (PET) particles in the presence and absence of seawater, and to explore the selection and enrichment of putative PET-active enzymes using gene- and genome-resolved metagenomics. The incubation conditions in the microcosms led to a gradual increase in desiccation and salinity. Consequently, halophilic taxa, including spore-forming bacteria and archaeal species (e.g., Halobacteriales ), were selectively enriched, particularly in seawater-depleted treatments. Lignocellulose input was the main factor restructuring the mangrove soil microbial communities, followed by seawater presence. In dry, lignocellulose-amended microcosms (L treatment), microbial diversity was significantly reduced, while lignocellulolytic species belonging to the phyla Bacillota and Actinomycetota were markedly enriched. Moreover, twelve putative PET hydrolases (PETases) were identified from the L treatment. These proteins shared > 70% sequence similarity with known PET-active enzymes, and three actinobacteria-derived enzymes were predicted to be thermostable, with melting temperatures ranging from 60–67°C. Two predictive PETases belonging to Microbulbifer species displayed distinct sequence and structural features compared to known PET-active enzymes, thereby extending the limited sequence landscape of existing PETases. This study demonstrates the potential of leveraging environmental microbiomes perturbed with plant-derived polymers as a strategy for capturing PETases.

Temperature has an overriding impact on microbial physiology, but the molecular basis of thermal acclimation in many ecologically relevant marine bacterial taxa remains unexplored. We used quantitative transcriptomics to analyse the transcriptional reprogramming of a proteorhodopsin‐based photoheterotroph, Dokdonia sp. MED134, during thermal acclimation from 10°C to 34°C. Temperature significantly impacted the expression of most MED134 genes (84%). Marker genes of the general stress response were induced towards cold temperature (10°C). Conversely, highly expressed genes associated with DNA replication and resource acquisition, like TonB‐dependent transporters and gliding motility genes, were upregulated towards warm temperatures along this thermal range, when growth rates were fast. The mRNA transcript abundance of most genes related to the TCA cycle was not differentially expressed by temperature. By contrast, the expression of genes associated with anaplerotic carbon fixation was significantly enhanced at the optimum growth temperature (25°C). The expression of the proteorhodopsin was minimum at 10°C, and its regulation by light was impaired at 34°C, suggesting regulatory imbalances in this key phototrophic gene under supra‐optimal warm conditions. Our findings highlight potential implications of growth temperature for regulating mechanisms of nutrient and energy acquisition, as well as the intracellular carbon flux in globally abundant marine photoheterotrophs.

Marine microorganisms are central to global ecological and biogeochemical systems, with their intricate interactions shaping community dynamics. While meta-omics data sets have revolutionized marine microbial ecology, they often provide fragmented insights, underscoring the need for advanced integrative modeling frameworks. In this review, we highlight the potential that community genome-scale metabolic models (cGEMs), in combination with meta-omics and environmental data sets, offer in advancing marine microbial ecology. We explore 3 key applications: quantifying marine ecosystem services, guiding bioremediation strategies for environmental challenges, and enhancing climate and biogeochemical models. Furthermore, we propose novel indices derived from cGEMs to assess microbial contributions to ecosystem functions, potentially informing economic valuation strategies for marine conservation. This interdisciplinary approach paves the way for innovative strategies in biotechnology, environmental restoration, and the development of nature-aligned economic systems, ultimately contributing to the preservation and sustainable use of marine ecosystems.

Temperature stands as one of the key factors influencing the community structure and distribution of marine microorganisms. Yet, the physiological adaptations of marine bacteria to rising temperatures remain underexplored. This study examines the transcriptional response of Dokdonia sp. MED134, a proteorhodopsin-based phototrophic organism within the class Flavobacteriia , to a gradient of temperature acclimation conditions from 10 to 34°C. Light availability during day/night cycles exerted minimal influence on the transcriptional patterns of this strain, with only a few genes mostly related to light sensing, light protecting mechanisms and phototrophy being upregulated during daytime. By contrast, temperature significantly impacted the expression of a large fraction of MED134 genes (>60%), including components of the stress response, cellular translation, DNA replication, and some metabolic pathways such as the anaplerotic carbon fixation and the glyoxylate shunt, suggesting intracellular carbon flow adjustments to temperature. Notably, the expression of some highly expressed TonB transporters, prominent in flavobacteria, was also temperature-sensitive. Our findings provide insights into the transcriptional adjustments of Dokdonia sp. MED134 in response to temperature variations, suggesting potential implications for carbon cycling and organic matter processing in marine environments.

The ecological role of microorganisms is of utmost importance due to their multiple interactions with the environment. However, assessing the contribution of individual taxonomic groups has proven difficult despite the availability of high throughput data, hindering our understanding of such complex systems. Here, we propose a quantitative definition of guild that is readily applicable to metagenomic data. Our framework focuses on the functional character of protein sequences, as well as their diversifying nature. First, we discriminate functional sequences from the whole sequence space corresponding to a gene annotation to then quantify their contribution to the guild composition across environments. In addition, we identify and distinguish functional implementations, which are sequence spaces that have different ways of carrying out the function. We demonstrate the value of our approach with two case studies: the ammonia oxidation and polyamine uptake guilds from the Malaspina circumnavigation cruise, revealing novel ecological dynamics of the latter in marine ecosystems. Thus, the quantification of guilds helps to assess the functional role of different taxonomic groups with profound implications on the study of microbial communities.

Prochlorococcus is a major marine primary producer with a global impact on atmospheric CO ₂ fixation. This cyanobacterium is widely distributed across the temperate ocean, but virtually absent at latitudes above 40° for yet unknown reasons.

The deep ocean (>200 m depth) is the largest habitat on Earth. Recent evidence suggests sulfur oxidation could be a major energy source for deep ocean microbes. However, the global relevance and the identity of the major players in sulfur oxidation in the oxygenated deep-water column remain elusive. Here we combined single-cell genomics, community metagenomics, metatranscriptomics and single-cell activity measurements on samples collected beneath the Ross Ice Shelf in Antarctica to characterize a ubiquitous mixotrophic bacterial group (UBA868) that dominates expression of RuBisCO genes and of key sulfur oxidation genes. Further analyses of the gene libraries from the ‘Tara Oceans’ and ‘Malaspina’ expeditions confirmed the ubiquitous distribution and global relevance of this enigmatic group in the expression of sulfur oxidation and dissolved inorganic carbon fixation genes across the global mesopelagic ocean. Our study also underscores the unrecognized importance of mixotrophic microbes in the biogeochemical cycles of the deep ocean.

Biological networks across scales exhibit hierarchical organization that may constrain network function. Yet, understanding how these hierarchies arise due to the operational constraint of the networks and whether they impose limits to molecular phenotypes remains elusive. Here we show that metabolic networks include a hierarchy of reactions based on a natural flux ordering that holds for every steady state. We find that the hierarchy of reactions is reflected in experimental measurements of transcript, protein and flux levels of Escherichia coli under various growth conditions as well as in the catalytic rate constants of the corresponding enzymes. Our findings point at resource partitioning and a fine-tuning of enzyme levels in E. coli to respect the constraints imposed by the network structure at steady state. Since reactions in upper layers of the hierarchy impose an upper bound on the flux of the reactions downstream, the hierarchical organization of metabolism due to the flux ordering has direct applications in metabolic engineering. Metabolism results from the activity of thousands of biochemical reactions, which create, transform and recycle all chemicals, i.e., metabolites, required by life. Metabolic reactions depend on enzymes—proteins acting as biological catalyzers—to proceed, which effectively links metabolism to other layers in the organization of cellular physiology, such as transcription and translation. These reactions do not operate in isolation but interact in a metabolic network due to the metabolites they share. The joint action of the reactions imposes constraints on the reaction fluxes denoting rates of conversion between metabolites. Here, we identify one such constraint imposed by the metabolic network of E. coli, which we call the flux order relation. Specifically, we identify pairs of reactions in which one reaction always carries a higher flux than the other at steady state. Hence, the flux order relation creates a hierarchical organization of metabolism. We show that the flux order relation is reflected in experimental data sets of fluxes, gene expression, protein levels, and enzyme catalytic constants. Our results point at resource partitioning and a fine-tuning of enzyme levels in E. coli to respect the flux order relation.