Tânia Aires

The use of microalgae-based photobioreactors (PBRs) offers a promising alternative for the sustainable tertiary treatment of urban wastewater. While the role of bacteria in such systems is well studied, the diversity and ecological function of eukaryotic communities remain poorly understood. Here, we used 18S rRNA gene amplicon sequencing to characterize eukaryotic diversity in outdoor PBRs fed with real wastewater operated with two hydraulic retention times (HRT), of 24 and 48h, over four seasons which presented distinct climate drivers (temperature, light intensity and rainfall). Our results revealed strong seasonal structuring of the communities, shaped by predator–prey interactions and temperature-dependent selection, while HRT had no significant impact. High temperatures and light intensity favoured thermotolerant microalgae such as Chlorella, likely due to reduced grazer pressure, and coincided with the highest phosphate removal which was likely performed by Chlorella under phosphorus depletion conditions. In contrast, seasons with mild temperatures, like spring, showed a peak in rotifer abundance and low microalgal biomass, correlating with enhanced biogas and methane production, as well as improved ammonium removal—possibly driven by rotifer-mediated nutrient cycling. In seasons characterized by lower temperatures and more abundant rainfall, communities were more balanced, with co-occurrence of chlorophytes (Tetradesmus and Desmodesmus) and predators such as rotifers and amoebae. However, nutrient removal efficiency declined during these seasons, likely due to increased rainfall-driven dilution and reduced phosphorus uptake under suboptimal N:P ratios. Correlation network analyses highlighted season-specific interactions among taxa, reflecting complex ecological dynamics. These findings demonstrate the critical role of eukaryotic communities in influencing both biomass composition and nutrient removal, offering valuable insights for the seasonal optimization of PBR performance in wastewater treatment.

Seagrass seedlings are key to meadow recovery under global change, as they enable recolonization of degraded areas and provide genetic variability needed for adaptation. While invasive macroalgae increasingly threaten seagrass communities, elevated CO2 has been proposed to enhance seagrass performance and potentially buffer other stressors. Here, we conducted a mesocosm experiment to test the combined effects of two invasive macroalgae (Lophocladia trichoclados and Caulerpa cylindracea) and elevated CO2 on Posidonia oceanica seedlings. CO2 enrichment increased carbohydrate reserves in rhizomes and induced subtle shifts in root-associated microbiomes. In contrast, invasive macroalgae had consistently negative effects on seedling development and physiology and strongly altered both above- and belowground microbial communities. Despite its potential to stimulate seagrass productivity, elevated CO2 did not mitigate the detrimental impacts of invasive macroalgae. These findings indicate that future CO2 conditions may not offset invasion-driven stress at the recruitment stage, highlighting the need for targeted management efforts to limit macroalgal proliferation and support seagrass meadow regeneration.

Global blue carbon assessments are hindered by a lack of data from understudied seagrass regions, such as those of Western Africa. This study reports the first in situ records of organic carbon (OC) stocks and burial rates for seagrass beds at Arguin Island, Banc d'Arguin (Mauritania), Western Africa, measured in intertidal Zostera noltei and subtidal Cymodocea nodosa meadows. The major blue carbon sources in seagrass meadows since 1900 were assessed using sedimentary environmental DNA (eDNA) and chronostratigraphy. The OC stocks in the top 50 cm of the sediment cores were not significantly different between the beds of the two seagrass species and averaged 27.8 ± 7.14 Mg C ha⁻¹, which is 5 times higher than that in adjacent unvegetated sediments. The OC sequestration rate for the past 100 years was 10.3 ± 1.4 g C m⁻² year⁻¹ in C. nodosa sediments and 12.3 ± 5.9 g C m⁻² year⁻¹ in Z. noltei sediments. Sedimentary eDNA analysis revealed that the major OC source within the C. nodosa and Z. noltei sediments has been the seagrass species itself, with low contributions from allochthonous eDNA reads. Carbon sources in Z. noltei meadows were more diverse than those in C. nodosa meadows. In bare sediment, diatoms were the major carbon source. The present study demonstrates the potential of sedimentary eDNA to reveal the major sources of organic matter in blue carbon ecosystems, improving our understanding of the provenance of sedimentary OC and thus carbon cycling processes. Additionally, it provides new OC stock and sequestration rate measurements from a region of the world that remains underrepresented in global blue carbon assessments.

Here, we present the draft genome sequence of Alteromonas gracilis strain J4, isolated from the green macroalga Caulerpa prolifera . The draft genome is 4,492,914 bp in size and contains 4,719 coding DNA sequences, 67 tRNAs, and 16 rRNA-coding genes. Strain J4 may exhibit host growth-promoting properties.

Persistently high marine temperatures are escalating and threating marine biodiversity. The Baltic Sea, warming faster than other seas, is a good model to study the impact of increasing sea surface temperatures. Zostera marina, a key player in the Baltic ecosystem, faces susceptibility to disturbances, especially under chronic high temperatures. Despite the increasing number of studies on the impact of global warming on seagrasses, little attention has been paid to the role of the holobiont. Using an outdoor benthocosm to replicate near‐natural conditions, this study explores the repercussions of persistent warming on the microbiome of Z. marina and its implications for holobiont function. Results show that both seasonal warming and chronic warming, impact Z. marina roots and sediment microbiome. Compared with roots, sediments demonstrate higher diversity and stability throughout the study, but temperature effects manifest earlier in both compartments, possibly linked to premature Z. marina die‐offs under chronic warming. Shifts in microbial composition, such as an increase in organic matter‐degrading and sulfur‐related bacteria, accompany chronic warming. A higher ratio of sulfate‐reducing bacteria compared to sulfide oxidizers was found in the warming treatment which may result in the collapse of the seagrasses, due to toxic levels of sulfide. Differentiating predicted pathways for warmest temperatures were related to sulfur and nitrogen cycles, suggest an increase of the microbial metabolism, and possible seagrass protection strategies through the production of isoprene. These structural and compositional variations in the associated microbiome offer early insights into the ecological status of seagrasses. Certain taxa/genes/pathways may serve as markers for specific stresses. Monitoring programs should integrate this aspect to identify early indicators of seagrass health. Understanding microbiome changes under stress is crucial for the use of potential probiotic taxa to mitigate climate change effects. Broader‐scale examination of seagrass–microorganism interactions is needed to leverage knowledge on host–microbe interactions in seagrasses.

Over 90% of introduced marine species are seaweeds. Seaweeds rely on their microbiome for host settlement, nutrition, development and health. As such, it is likely that microbiomes are involved in seaweed invasions. Sargassum muticum, indigenous to Southeast Asia, inhabits the North-east Atlantic from Norway to Morocco. This is the only known successful case of a non-clonal marine invader with almost no genetic variation over its large NE Atlantic introduced range. This makes it a very interesting model to study an invasive seaweeds microbiome, as it practically uncouples host genetic variation from microbiome variation. Associated bacteria potentially contribute to the plasticity and acclimation of S. muticum leading to its success over the last 50 years. Dispersing host organisms can either bring their acquired microbes along or obtain new ones locally, following the mutualist and generalist host hypothesis, respectively. We used partial 16S rRNA gene amplicon sequencing to characterize the total and core microbiome across S. muticum structures/tissues from five NE Atlantic regions, from Norway to Morocco, covering over 30° of latitude. In contrast to host genotypes, highly diverse, regional, total and core microbiomes, with differentiation levels depending on tissue, bacterial community structure were detected. Atlantic S. muticum follows the generalist host hypothesis, possibly recruiting a new microbiome in each new region. This host promiscuity may promote the invasiveness of S. muticum. Diversity was lower in the young/annual tissues compared with the older tissues for the total bacterial community, suggesting that these are mostly transitory bacteria accumulating over time in the older parts. The total core microbiome included 10 OTUs, representing dominant community members commonly found in other seaweeds’ cores. The core Granulosicoccus OTU followed a clear regional pattern where northern and southern regions clustered differentially, suggesting a regional signature even at an OTU level.

Macroalgae play an intricate role in microbial-mediated coral reef degradation processes due to the release of dissolved nutrients. However, temporal variabilities of macroalgal surface biofilms and their implication on the wider reef system remain poorly characterized. Here, we study the microbial biofilm of the dominant reef macroalgae Sargassum over a period of one year at an inshore Great Barrier Reef site (Magnetic Island, Australia). Monthly sampling of the Sargassum biofilm links the temporal taxonomic and putative functional metabolic microbiome changes, examined using 16S rRNA gene amplicon and metagenomic sequencing, to the pronounced growth-reproduction-senescence cycle of the host. Overall, the macroalgal biofilm was dominated by the heterotrophic phyla Firmicutes (35% ± 5.9% SD) and Bacteroidetes (12% ± 0.6% SD); their relative abundance ratio shifted significantly along the annual growth-reproduction-senescence cycle of Sargassum. For example, Firmicutes were 1.7 to 3.9 times more abundant during host growth and reproduction cycles than Bacteroidetes. Both phyla varied in their carbohydrate degradation capabilities; hence, temporal fluctuations in the carbohydrate availability are potentially linked to the observed shift. Dominant heterotrophic macroalgal biofilm members, such as Firmicutes and Bacteroidetes, are implicated in exacerbating or ameliorating the release of dissolved nutrients into the ambient environment, though their contribution to microbial-mediated reef degradation processes remains to be determined.

Invasive plants, including marine macrophytes, are one of the most important threats to biodiversity by displacing native species and organisms depending on them. Invasion success is dependent on interactions among living organisms, but their study has been mostly limited to negative interactions while positive interactions are mostly underlooked. Recent studies suggested that microorganisms associated with eukaryotic hosts may play a determinant role in the invasion process. Along with the knowledge of their structure, taxonomic composition, and potential functional profile, understanding how bacterial communities are associated with the invasive species and the threatened natives (species-specific/environmentally shaped/tissue-specific) can give us a holistic insight into the invasion mechanisms. Here, we aimed to compare the bacterial communities associated with leaves and roots of two native Caribbean seagrasses (Halodule wrightiiandThalassia testudinum) with those of the successful invaderHalophila stipulacea, in the Caribbean island Curaçao, using 16S rRNA gene amplicon sequencing and functional prediction. Invasive seagrass microbiomes were more diverse and included three times more species-specific core OTUs than the natives. Associated bacterial communities were seagrass-specific, with higher similarities between natives than between invasive and native seagrasses for both communities associated with leaves and roots, despite their strong tissue differentiation. However, with a higher number of OTUs in common, the core community (i.e., OTUs occurring in at least 80% of the samples) of the nativeH. wrightiiwas more similar to that of the invaderH. stipulaceathanT. testudinum, which could reflect more similar essential needs (e.g., nutritional, adaptive, and physiological) between native and invasive, in contrast to the two natives that might share more environment-related OTUs. Relative to native seagrass species, the invasiveH. stipulaceawas enriched in halotolerant bacterial genera with plant growth-promoting properties (likeHalomonassp. andLysinibacillussp.) and other potential beneficial effects for hosts (e.g., heavy metal detoxifiers and quorum sensing inhibitors). Predicted functional profiles also revealed some advantageous traits on the invasive species such as detoxification pathways, protection against pathogens, and stress tolerance. Despite the predictive nature of our findings concerning the functional potential of the bacteria, this investigation provides novel and important insights into native vs. invasive seagrasses microbiome. We demonstrated that the bacterial community associated with the invasive seagrassH. stipulaceais different from native seagrasses, including some potentially beneficial bacteria, suggesting the importance of considering the microbiome dynamics as a possible and important influencing factor in the colonization of non-indigenous species. We suggest further comparison ofH. stipulaceamicrobiome from its native range with that from both the Mediterranean and Caribbean habitats where this species has a contrasting invasion success. Also, our new findings open doors to a more in-depth investigation combining meta-omics with bacterial manipulation experiments in order to confirm any functional advantage in the microbiome of this invasive seagrass.

The input of nutrients from anthropogenic sources is the leading cause of coastal eutrophication and is usually coupled with algal/seaweed blooms. Effects may be magnified in semi-enclosed systems, such as highly productive coastal lagoon ecosystems. Eutrophication and seaweed blooms can lead to ecosystem disruption. Previous studies have considered only one of these factors, disregarding possible interactive effects and the effect of the blooming species’ identity on sediment bacterial communities. We tested the effect of experimental nutrient loading and two common blooming seaweeds (Ulva rigida and Gracilaria vermiculophylla) in coastal lagoon sediments, on the structure of bacterial communities (using 16S rRNA amplicon sequencing) and corresponding putative functional potential (using PiCRUSt). At the Operational Taxonomic Unit (OTU) level, the addition of nutrients reduced bacterial community α-diversity and decreased the abundance of sulfate reducers (Desulfobacterales) compared to sulfur oxidizers/denitrifiers (Chromatiales and Campylobacterales), whereas this was not the case at the order level. Seaweed addition did not change bacterial α-diversity and the effect on community structure depended on the taxonomic level considered. The addition of Gracilaria increased the abundance of orders and OTUs involved in sulfate reduction and organic matter decomposition (Desulfobacterales, Bacteroidales, and Clostridiales, respectively), an effect which was also detected when only Ulva was added. Nutrients and the seaweeds combined only interacted for Ulva and nutrients, which increased known sulfide oxidizers and denitrifiers (order Campylobacterales). Seaweed enrichment affected putative functional profiles; a stronger increase of sulfur cycling KEGG pathways was assigned to nutrient-disturbed sediments, particularly with the seaweeds and especially Ulva. In contrast, nitrogen and sulfur cycle pathways showed a higher abundance of genes related to dissimilatory nitrate reduction to ammonium (DNRA) in Ulva+nutrients treatments. However, the other seaweed treatments increased the nitrogen fixation genes. Thiosulfate reduction, performed by sulfate-reducing bacteria, increased in seaweed treatments except when Ulva was combined with nutrients. In conclusion, the in situ addition of nutrients and the seaweeds to intertidal sediments affected the bacterial communities differently and independently. The predicted functional profile suggests a shift in relative abundances of putative pathways for nitrogen and sulfur cycles, in line with the taxonomic changes of the bacterial communities.

Seaweed-associated microbiota experience spatial and temporal shifts in response to changing environmental conditions and seaweed physiology. These shifts may result in structural, functional and behavioral changes in the host with potential consequences for its fitness. They, thus, may help the host to adapt to changing environmental conditions. The current knowledge of seasonal variation of seaweed-associated microbiota is however still limited. In this study, we explored temporal and spatial variation of microbial communities associated with the invasive brown seaweed S. muticum. We sampled in northern and southern Portugal, in September, March and July-August (summer). In addition, as (pseudo-)perennial seaweeds display seasonal reproductive phenology, we sampled various parts of the individuals to disentangle the effect of temporal changes from those due to structural development variations. The diversity and structure of associated microbial communities were determined using next generation sequencing of the variable regions V5-7 of the 16S rDNA. We expected to find differentiation in associated microbial communities between regions and sampling months, but with differences depending on the seaweed structure examined. As expected, the study revealed substantial temporal shifts in S. muticum microbiome, for instance with large abundance of Rhodobacteraceae and Loktanella in September-March but prevalence of Pirellulales during the summer months. Variations between regions and tissues were also observed: in northern Portugal and on basal structures, bacterial diversity was higher as compared to the South and apical parts. All examined seaweed structures showed temporal differences in associated microbial community structure over time, except for holdfasts between September and March. Bacteria contributing to these changes varied spatially. Conversely to all other structures, the holdfast also did not show differences in associated community structure between southern and northern regions. Our study highlights the importance of structural microscale differentiations within seaweeds hosts with regard to their associated microbial communities and their importance across temporal and spatial dimensions.