Biology subjects

Villena-Alemany, C.

Publications and source records attributed to Villena-Alemany, C..

6 recordsLinked to original sources

bioRxiv2025

Thermophilic bacteria employ a contractile injection system in hot spring microbial mats

Bacterial contractile injection systems (CISs) are multiprotein complexes that facilitate the bacterial response to environmental factors or interactions with other organisms. Multiple novel CISs have been characterised in laboratory bacterial cultures recently; however, studying CISs in the context of the native microbial community remains challenging. Here, we present an approach to characterise a new, bioinformatically predicted CIS by directly analysing bacterial cells from their natural environment. Using cryo-focused ion beam milling and cryo-electron tomography (cryoET) imaging, guided by 16S amplicon sequencing, we discovered that thermophilic Chloroflexota bacteria produce intracellular CIS particles in a natural microbial hot spring mat. We then found a niche-specific production of CIS in the structured microbial community using an approach combining shotgun metagenomics, proteomics, and immunogold staining. Bioinformatic analysis and imaging revealed CISs in other extremophilic Chloroflexota and Deinococcota. This Chloroflexota/Deinococcota CIS lineage shows phylogenetic and structural similarity to previously described cytoplasmic CIS from Streptomyces and probably shares the same cytoplasmic mode of action. Our integrated environmental cryoET approach is suitable for discovering and characterising novel macromolecular complexes in environmental samples.

microbiology↗

bioRxiv2025

Particle attachment drives seasonal abundance and photoheterotrophy of marine aerobic anoxygenic phototrophs

BackgroundAerobic Anoxygenic Phototrophic (AAP) bacteria are an essential component of aquatic microbial communities and play an important role in carbon cycling due to their ability to supplement their chemoorganotrophic metabolism with light-derived energy. While most of the previous studies focused on abundance, species composition and seasonal changes of AAP bacteria, their affinity for the particle-attachment did not attract much attention. Similarly, it remains unclear whether the entire AAP community is phototrophically active. This study investigated the seasonal changes in the composition of free-living and particle-attached AAP bacteria in the central Adriatic Seas coastal waters using both DNA and RNA pufM amplicon gene sequencing in the particle-attached and the free-living fractions. ResultsAAP bacterial abundance grew from 1.27 x 104 cells mL-1 in winter to 8.30 x 104 cells mL-1 in summer. The proportion of AAP bacteria was consistently higher in the particle-attached fraction, particularly in spring and summer. DNA and RNA pufM amplicon analyses revealed large differences in activity among the species forming the AAP communities. Additionally, DNA-based assessments underestimated the phototrophic activity of certain genera, demonstrating discrepancies between the gene presence and its functional activity. ConclusionsOur data demonstrated that the expression of phototrophic genes in AAP bacteria is not uniform and largely varies throughout seasons and fractions. The particle-attached fraction harboured more than twice as many active AAP bacteria as the free-living fraction, with seasonal shifts and lifestyle driving changes in the phototrophy gene expression. RNA and DNA libraries revealed discrepancies between total and active AAP bacterial communities, emphasizing the necessity of transcript-based approaches for accurately assessing photoheterotrophic activity in marine environments. The pronounced partitioning of AAP bacterial diversity and activity between free-living and particle-attached fractions indicated the ecological specialization of certain AAP lineages, which may have noteworthy implications for the consumption of particulate organic matter and, ultimately, carbon cycling in coastal waters.

microbiology↗

bioRxiv2024

Effects of excess phosphate on a coastal plankton community

Eutrophication in the Baltic Sea has caused an imbalance in the inorganic nitrogen (N) to phosphorus (P) ratio, leaving excess phosphate (PO4) after the phytoplankton spring bloom that terminates after N-depletion. Using monitoring data, we demonstrated that the PO4 concentration has continued to increase in the outermost Gulf of Finland during past decades. We further investigated the fate of such excess PO4 in a two-week mesocosm (1.2 m3) experiment. The starting concentration of PO4 was 0.66 {micro}M, and treatments included a non-treated control (control), nitrate addition (N-add; 3.6 {micro}M), glucose addition (C-add; 25 {micro}M) and combined nitrate and glucose addition (N+C-add). The addition of N both in N-add and N+C-add treatments stimulated nano- and microphytoplankton, while the picophytoplankton abundance increased only after N-depletion. Also, the copepod biomass was positively affected by the N-addition. N2-fixing cyanobacteria were present but in low abundance. Carbon addition did not enhance heterotrophic bacterial uptake of PO4 contrary to our expectations, nor did it affect the phyto- or zooplankton community composition. The PO4 concentration was reduced to [~]0.4 {micro}M in the control and C-add treatments and to 0.16 {micro}M in the two N-amended treatments, with an inorganic N:P uptake ratio of 6.7. These results underscore the role of picophytoplankton in reducing the excess PO4 pool after the spring bloom, a function traditionally ascribed to bloom-forming diazotrophic cyanobacteria in the Baltic Sea.

microbiology↗

bioRxiv2024

Microbial remineralization processes during post-spring-bloom excess phosphate in the northern Baltic Sea

In the northern Baltic, post-spring-bloom low dissolved inorganic nitrogen to phosphorus conditions, degradation of N-rich organic matter potentially supports the drawdown of excess phosphate. During a 17-day-long mesocosm experiment in the south-west Finnish archipelago, we examined nitrogen, phosphorus and carbon acquiring extracellular enzyme activities in three size fractions (<0.2 {micro}m, 0.2-3 {micro}m, and >3 {micro}m), bacterial abundance, production, community composition and its predicted metabolic functions. The mesocosms received different carbon and nitrogen amendments to test for the effect of inorganic nutrient stoichiometry on enzymatic degradation processes that ultimately determine the export potential of organic matter. Alkaline phosphatase activity occurred mainly in the dissolved form and likely contributed to the excess phosphate conditions. In the beginning of the experiment, peptidolytic and glycolytic enzymes were predicted to be produced by free-living bacteria identified within the classes Actinobacteria and Alphaproteobacteria, whereas the contribution of picocyanobacteria increased towards the end. Our results imply that heterotrophic bacteria lost the competition to picocyanobacteria due to the lack of suitable energy sources. The high hydrolytic rates in fractions <0.2 {micro}m and 0.2-3 {micro}m, found in this study, could potentially retain inorganic nutrients in the surface layer and suppress downward fluxes of organic matter and hence carbon sequestration.

microbiology↗

bioRxiv2023

Winners in good times and bad times: Aerobic anoxygenic phototrophic bacteria profit from photoheterotrophy under carbon-rich and poor conditions

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/572764v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1e52797org.highwire.dtl.DTLVardef@18a568forg.highwire.dtl.DTLVardef@138e2c5org.highwire.dtl.DTLVardef@1b0224c_HPS_FORMAT_FIGEXP M_FIG C_FIG Aerobic Anoxygenic Phototrophic (AAP) bacteria are an important component of freshwater bacterioplankton. They can support their heterotrophic metabolism with energy from light, and by that enhance their growth efficiency. Based on results from cultures, it was hypothesized that photoheterotrophy provides an advantage under carbon limitation and facilitates access to recalcitrant or low-energy carbon sources. However, verification of these hypotheses for natural AAP communities has been lacking. Here, we conducted whole community manipulation experiments and compared the growth of AAP bacteria under carbon limited and with recalcitrant or low-energy carbon sources under dark and light conditions to elucidate how they profit from photoheterotrophy. We found that it depends on the season. In spring, AAP bacteria induce photoheterotrophic metabolism under carbon limitation but they outperform heterotrophic bacteria when carbon is available. This effect seems to be driven by physiological responses rather than changes at the community level. In autumn photoheterotrophy is less beneficial. In both seasons, AAP bacteria responded negatively to recalcitrant or low-energy carbon sources in light. This unexpected observation may have ecosystem-level consequences as lake browning continues. In general, our findings contribute to the understanding of the dynamics of AAP bacteria observed in pelagic environments.

ecology↗

bioRxiv2023

Phenology and ecological role of Aerobic Anoxygenic Phototrophs in fresh waters

Aerobic anoxygenic phototrophic (AAP) bacteria are heterotrophic bacteria that supply their metabolism with light energy harvested by bacteriochlorophyll-a-containing reaction centres. Despite their substantial contribution to bacterial biomass, microbial food webs and carbon cycle, their phenology in freshwater lakes remains unknown. Hence, we investigated seasonal variations of AAP abundance and community composition biweekly across three years in a temperate, meso-oligotrophic freshwater lake. AAP bacteria displayed a clear seasonal trend with a spring maximum following the bloom of phytoplankton and a secondary maximum in autumn. As the AAP bacteria represent a highly diverse assemblage of species, we followed their seasonal succession using the amplicon sequencing of the pufM marker gene. To enhance the accuracy of the taxonomic assignment, we developed new pufM primers that generate longer amplicons and compiled the currently largest database of pufM gene, comprising 3633 reference sequences spanning all phyla known to contain AAP species. With this novel resource we demonstrated recurrent and dynamic seasonal succession of the AAP community. The majority of the species appeared during specific phases of the seasonal cycle, with less than 2% of AAP species detected during the whole year. Our results document the indigenous freshwater nature of the AAP community, characterized by high resilience and heterogenic adaptations to varying conditions of the freshwater environment. By integrating this information with the indicator of primary production (Chlorophyll-a) and existing ecological models, we show that AAP bacteria play a pivotal role in the recycling of dissolved organic matter released during spring phytoplankton bloom, contributing significantly to the ecological dynamics of lakes.

microbiology↗