Las Tablas de Daimiel National Park is no ordinary nature reserve. Covering roughly 20 square kilometers in the floodplain of the Cigüela and Guadiana rivers, it represents one of the last river floodplains in southern Europe. The park sits at the heart of the UNESCO-designated La Mancha Húmeda Biosphere Reserve and is also a Ramsar wetland site of international importance. Yet despite these protections, the ecosystem has been under siege. Until the mid-1980s, the wetland functioned as the natural groundwater discharge of the Western La Mancha Aquifer, which is now severely overexploited due to intensive extraction for irrigated agriculture. Combined with high organic inputs from untreated wastewater and agricultural runoff, this has transformed the park into a hydrologically fluctuating, hypertrophic system with elevated concentrations of toxic trace elements in its sediments.

Wetlands around the world are in similar trouble. These ecosystems cover approximately 13.4 percent of the global land area outside Antarctica and serve as critical biodiversity shelters, hosting everything from migratory birds to rare and endangered plants. But recent estimates suggest that more than half of the world’s original wetland area has already been lost, driven primarily by urbanization, agricultural expansion, and cumulative water pollution. As these landscapes decline, microbial communities have emerged as one of the most sensitive and accurate indicators of ecosystem health, responding rapidly to anthropogenic impacts across freshwater bodies worldwide.

Against this backdrop, the research team set out to provide a comprehensive snapshot of the prokaryotic life at Las Tablas de Daimiel. On May 30, 2023, they collected six samples across four different stations within the park: Entradilla, Casilla de Benito, Puente Navarro, and El Tablazo. At each location, they gathered samples from both the water column and the sediments, with El Tablazo being completely dry at the time of sampling. Water was collected in acid-washed polyethylene bottles from the surface of the ponds, while sediment samples were extracted by hand using a core sampler. Alongside the biological sampling, the team measured a full suite of environmental parameters in situ, including temperature, dissolved oxygen, pH, conductivity, major cations, nutrients, and carbon fractions.

Back in the laboratory, DNA was extracted from all samples using a DNeasy PowerSoil kit, and the material was sent to the FISABIO Sequencing and Bioinformatics Service in Valencia, Spain. There, two amplicon libraries per sample were created through PCR amplification, one targeting the bacterial V3-V4 region of the 16S rRNA gene and the other targeting the archaeal V3-V5 region. Specific primer pairs were used for each domain, and the resulting libraries were sequenced on an Illumina Nextseq2000 P1 platform using paired-end sequencing at 2×300 base pairs. The raw reads were then processed through the DADA2 pipeline in R, where trimming, chimera removal, and taxonomic classification against the SILVA rRNA database were performed to generate a final table of Amplicon Sequence Variants, or ASVs.

The results are striking. After quality control and the removal of contamination and potential chimeras, the dataset totals 19,855 bacterial ASVs grouped into 64 phyla and 1,766 archaeal ASVs grouped into 11 phyla. The prokaryotic diversity captured in this study surpasses that of previous amplicon surveys at the park, underscoring the scope of the analysis. Only 106 bacterial ASVs are common to all six samples, spanning 12 different phyla including Proteobacteria, Firmicutes, Actinobacteriota, Cyanobacteria, and Planctomycetota. For Archaea, just two ASVs classified to the phylum Crenarchaeota are shared across all stations. The lowest number of ASVs was detected in the Entradilla water sample, with 2,000 total, while the largest number, 12,107, came from the Casilla de Benito sediment sample.

Perhaps the most remarkable finding is the sheer proportion of unknown microbial life at the park. Up to 59.83 percent of the bacterial genera, representing 11,879 ASVs, remain undescribed, while this proportion reaches an extraordinary 88.56 percent of the archaeal genera, or 1,564 ASVs. These values are consistent with previous surveys showing that the uncultured microbial majority can represent up to 81 percent of microbial genera across ecosystems. Furthermore, 421 bacterial ASVs and 255 archaeal ASVs could not even be classified at the phylum level, suggesting that Las Tablas de Daimiel may host a relatively large collection of entirely unknown microbial taxa waiting to be discovered.

The study also reveals a clear taxonomic split between the microbial communities living in the water column and those in the sediments. For Archaea, the water column is dominated by the class Nanoarchaeia, mainly the order Woesearchaeales, along with various unclassified archaeal ASVs, while the sediments are characterized by Bathyarchaeia, Halobacteria, Nitrososphaeria, and Thermoplasmata. Bacterial differences are less pronounced but still noticeable: the water column is dominated by Actinobacteria, Bacteroidia, Cyanobacteriia, and Gammaproteobacteria, while the sediments harbor Alphaproteobacteria and Cyanobacteriia belonging primarily to the orders Phormidesmiales and Cyanobacteriales. Non-metric multidimensional scaling analysis confirmed that benthic samples cluster separately from pelagic samples for both domains, and Shannon and Simpson diversity indices showed higher bacterial richness in the benthic communities than in the pelagic ones.

The release of this dataset marks a significant step forward for the long-term environmental monitoring of Las Tablas de Daimiel National Park. By expanding the known benthic and pelagic diversity of both Archaea and Bacteria at the site, and by documenting the apparent taxonomic differentiation between these two habitats, the study provides a robust reference point against which future changes can be measured. As climate change, water extraction, and pollution continue to pressure wetlands across the globe, tools like 16S rRNA amplicon sequencing will become increasingly essential for tracking the invisible microbial communities that underpin ecosystem function. For this unique Spanish wetland, the newly published data offers a valuable resource for future conservation efforts aimed at improving the health and survival of one of Europe’s last great floodplain ecosystems.

Subject of Research: A 16S rRNA amplicon dataset of Las Tablas de Daimiel National Park, Spain

Article Title: A 16S rRNA amplicon dataset of Las Tablas de Daimiel National Park, Spain

Article References: Rodríguez-Gijón, A., López-Maroto, V., Mestre, M., Sánchez-Carrillo, S., & Laso-Pérez, R. (2026). A 16S rRNA amplicon dataset of Las Tablas de Daimiel National Park, Spain. Metabarcoding and Metagenomics, 10, Article e173083. https://doi.org/10.3897/mbmg.10.173083

Image Credits: AI Generated

DOI: 10.3897/mbmg.10.173083

Keywords: rRNA, amplicon, dataset, Tablas, Daimiel, National, Park, Spain, scientific research

The study, led by Edoardo Mandalà and Martina Coppini, enrolled twelve patients at the Oral Medicine Unit of the Paolo Giaccone Policlinico University Hospital in Palermo, Italy. Seven had confirmed oral squamous cell carcinoma, while five served as cancer-free controls, including two healthy individuals and two with oral leukoplakia, a potentially precancerous condition. After one control patient was identified as a biological outlier because their microbial profile clustered suspiciously close to the cancer group, eleven subjects remained in the final analysis. From each participant, the team collected paired samples: unstimulated morning saliva and a fresh fragment of tissue taken during incisional biopsy, frozen immediately at minus 80 degrees Celsius.

The technical core of the study was next-generation sequencing of the 16S ribosomal RNA gene, the workhorse marker of microbiome science. This gene contains hypervariable regions that act like molecular barcodes, allowing researchers to identify which bacteria are present in a sample. The team targeted the V1, V2, and V3 hypervariable regions, amplified them by polymerase chain reaction, and sequenced the libraries on an Illumina MiSeq platform. After taxonomic classification using the Illumina BaseSpace 16S Metagenomics app, more than 1.2 million species-classified reads were retained across the 22 analyzed samples, averaging roughly 55,000 classified reads per sample. That depth allowed the researchers to identify 1,711 unique bacterial species distributed across 737 genera, providing an unusually fine-grained census of the oral ecosystem in health and disease.

The first surprise was that the total number of bacterial species did not differ dramatically between cancer patients and controls. Alpha-diversity analysis, which measures species richness and evenness within a sample, showed no significant differences in saliva and only a trend toward higher diversity in tumor biopsies. But when the researchers examined beta diversity, which compares the overall structure of microbial communities between samples, a different story emerged. In saliva, the communities of cancer patients and controls looked largely similar, with no distinct clustering. In biopsy samples, however, the two groups separated noticeably along the primary axes of a principal coordinate analysis based on Bray-Curtis dissimilarity, with a statistical trend approaching significance. The dysbiotic shifts associated with cancer, in other words, are far more pronounced inside the tissue microenvironment than in the saliva bathing it.

At the genus level, the core microbiome of the cohort was dominated by Streptococcus, which accounted for nearly a quarter of all sequencing reads, followed by Prevotella and Neisseria. But the distribution of these genera across the four study groups revealed a striking reorganization. In control saliva, Streptococcus reigned at 28 percent abundance, while in cancer patients’ saliva it dropped to 17 percent, nearly matched by an expansion of Neisseria to 17 percent from just 4.4 percent in controls. In tissue, the contrast was even sharper. Control biopsies were heavily dominated by Streptococcus at 37 percent, whereas cancer biopsies showed Streptococcus reduced to 22 percent alongside a marked rise of Fusobacterium, which climbed from 1.7 percent in healthy tissue to 7.4 percent in tumors.

Resolving these genus-level shifts to the species level produced the study’s most consequential findings. In tumor tissue, Fusobacterium nucleatum, an anaerobic bacterium already infamous for its role in colorectal cancer, exhibited a 29-fold increase in abundance, rising from a negligible 0.2 percent in control tissues to 4.9 percent in tumors, a difference that reached nominal statistical significance. This pathogen is no passive bystander. Previous research has shown that it stimulates cancer cell proliferation through the E-cadherin and beta-catenin signaling pathway and promotes immune evasion by binding the TIGIT inhibitory receptor on host immune cells. Meanwhile, health-associated commensals were systematically eradicated: Streptococcus salivarius, the most abundant species in control biopsies at 11.5 percent, plummeted to 0.3 percent in tumors, while Streptococcus oralis fell from 8 percent to 1.4 percent. These streptococci normally maintain oral homeostasis by producing bacteriocins and hydrogen peroxide, so their loss represents a functional collapse of colonization resistance, potentially opening the door for opportunistic anaerobes to invade.

The salivary signature told a complementary but distinct story. In cancer patients’ saliva, Neisseria macacae surged tenfold, from 0.9 percent in controls to 9.8 percent, becoming the single most abundant species in the cancer salivary microbiome. Concurrently, Haemophilus parainfluenzae and Neisseria perflava rose, while the commensal Streptococcus salivarius collapsed from 9.4 percent to 1.6 percent. This finding is particularly intriguing because it suggests that saliva, far from being a perfect mirror of the tumor, reflects a broader ecosystem shift that could be exploited for non-invasive screening. The researchers propose that the imbalance between Streptococcus and Neisseria in saliva might serve as a candidate biomarker, distinct from the intratumoral pathogen load that requires a biopsy to measure.

Perhaps the most forward-looking result came from an exploratory analysis of Fusobacterium nucleatum sequence variants. In five of seven cancer patients, the tumor niche was dominated by a single 16S sequence variant corresponding to reference NR_117842.1, which maps to the type strain ATCC 25586 of the subspecies nucleatum. This strain is the model organism for Fusobacterium pathogenicity, known to express high levels of the FadA adhesin that binds E-cadherin on epithelial cells and activates beta-catenin signaling. In patients with the highest bacterial burden, this single variant accounted for more than 99 percent of all Fusobacterium reads, suggesting an active selection process driven by the malignant microenvironment rather than passive colonization. One patient instead carried a distinct dominant variant mapping to the subspecies vincentii, indicating that while the specific strain may vary between individuals, the functional requirement for a highly adhesive, virulent phenotype appears conserved. The authors caution that standard 16S sequencing lacks definitive strain-level resolution, so confirming true clonal expansion will require shotgun metagenomics or whole genome sequencing.

When the researchers mapped microbial profiles across the clinical disease continuum, from healthy mucosa through leukoplakia to early and advanced cancer, a staged ecological succession came into view. Fusobacterium remained at baseline levels in healthy tissue and leukoplakia lesions, then surged during early-stage tumors, reaching peaks of nearly 14 percent, before declining in advanced disease. Prevotella, by contrast, established a dominant presence in advanced-stage tumors, stabilizing at abundances above 10 percent. This pattern aligns with the driver-passenger model of tumor microbiology: Fusobacterium may act as an active driver in the initial phases of malignancy, anchoring itself to the nascent tumor through the Fap2 adhesin that binds Gal-GalNAc sugars overexpressed on transformed epithelial cells, while strict anaerobic passengers like Prevotella later colonize the hypoxic, necrotic core of the growing mass.

The authors are careful to frame these findings as hypothesis-generating rather than definitive. With only eleven analyzed subjects, the statistical power is limited, and several trends that appear biologically meaningful did not survive multiple testing corrections. The inclusion of leukoplakia patients in the control group adds biological heterogeneity, the lack of systematic periodontal indices precludes precise assessment of baseline dental health, and the cross-sectional design cannot establish whether microbial shifts cause cancer or merely accompany it. Yet the magnitude of the changes observed, particularly the 29-fold enrichment of Fusobacterium nucleatum in tumors and the near-total eradication of protective streptococci, provides a compelling preliminary signal. If validated in larger, longitudinal cohorts, this work could lay the foundation for a multi-marker diagnostic panel combining salivary microbial ratios with intratumoral pathogen quantification, and it adds momentum to a growing field exploring microbiome-based precision medicine in oncology, where engineered bacteria may one day be deployed to remodel the tumor microenvironment and enhance immunotherapy.

Subject of Research: Oral cancer tumors harbor a distinct dysbiotic bacterial ecosystem dominated by Fusobacterium nucleatum, while saliva shows a separate Neisseria-driven signature, according to a 16S rRNA sequencing pilot study.

Article Title: Analysis of 16S rRNA to evaluate taxonomic differences between salivary and intratumoral microbiota in patients affected by oral squamous cell carcinoma: a single-center pilot study

Article References: Mandalà, E., Coppini, M., Mauceri, R., Pizzo, M., Giammanco, G. M., Campisi, G., & Bonura, C. (2026). Analysis of 16S rRNA to evaluate taxonomic differences between salivary and intratumoral microbiota in patients affected by oral squamous cell carcinoma: a single-center pilot study. Frontiers in Bacteriology, 5, Article 1863255. https://doi.org/10.3389/fbrio.2026.1863255

Image Credits: AI Generated

DOI: 10.3389/fbrio.2026.1863255

Keywords: oral cancer, microbiome, Fusobacterium nucleatum, 16S rRNA sequencing, oral squamous cell carcinoma, tumor microenvironment, salivary biomarkers, dysbiosis, Analysis, rRNA, evaluate, taxonomic

The question matters because plankton death is not simply an endpoint. When plankton cells die, their decomposing remains release dissolved organic carbon into the surrounding seawater, a form of carbon that microbes can transform and that can be stored in the ocean for thousands of years. The fate of this carbon shapes everything from microbial food webs to the ocean’s long-term capacity to sequester greenhouse gases. Understanding the mechanisms behind plankton mortality is therefore essential for reconstructing how marine ecosystems function and how material flows through them. The trouble is that a single plankton community can consist of hundreds of coexisting species, and pinpointing how many cells within such a crowded assemblage are dying, and at what rate, has long eluded researchers.

A team at Kyoto University has now tackled this challenge by focusing on one of the most pervasive causes of plankton death: viral infection. Viruses are extraordinarily abundant in seawater, and when they infect a plankton cell they often trigger cell lysis, the process by which the cell’s membrane breaks down and its contents, including genetic material, spill into the environment. This invisible death releases ribosomal RNA, or rRNA, into the water. Rather than trying to count dying cells directly, the researchers reasoned that they could measure the RNA these cells leave behind, turning the genetic debris of viral lysis into a quantitative signal of mortality.

To build such a measurement, the team first grew laboratory cultures of two phytoplankton groups, diatoms and raphidophytes, in a seawater-based medium. They then extracted the rRNA present in the medium and quantified it using digital PCR, a highly sensitive technique capable of counting individual nucleic acid molecules. The approach faced a fundamental obstacle, however: rRNA released into seawater does not persist. It degrades over time, meaning that any measured concentration reflects both the ongoing production of cell-free rRNA and its simultaneous disappearance. Without accounting for degradation, the method would systematically underestimate how much RNA dying cells actually release.

The researchers solved this problem with an elegant trick borrowed from analytical chemistry. They introduced a culture of spike-in ribosomes, a known quantity of ribosomal material that was not produced by the plankton, into the medium and tracked how quickly it degraded. This gave them a degradation rate constant specific to their experimental conditions. They then built a flux model that incorporated both the measured changes in host cell-free rRNA over time and this degradation constant. With both terms in hand, the model could correct for the RNA that had already broken down, making it possible to estimate the true rate of cell lysis at any given moment in the experiment.

The results were striking. Viral infection enhanced the rate of cell-free rRNA production approximately 46-fold compared with uninfected cultures, and subsequent cell lysis boosted it roughly 302-fold. In the non-infected solutions, only very small amounts of rRNA were actively released by living cells, underscoring how strongly lysis signals stand out from the background noise of a healthy population. The method effectively turns viral mortality into a measurable molecular beacon, one that can be detected while the deaths themselves are happening.

Perhaps the most surprising finding emerged from the timing. In the diatom experiment, dissolved rRNA production peaked before the population density began to decline as a result of viral infection. In other words, active cell lysis was already underway while the population as a whole was still growing steadily. From a biogeochemical perspective, this implies that the supply of dissolved organic matter to the environment through cell death may occur primarily during the growth phase of a bloom, rather than during its apparent decline, as conventional observations would suggest. Cells are dying and leaking their contents into the water long before anyone watching the population curve would notice.

We did not expect the temporal decoupling between population declines and cell lysis, says corresponding author Hisashi Endo of Kyoto University. Observing the dynamics of living cells is not enough to evaluate the dissolved organic carbon that phytoplankton contribute to marine environments. The statement carries significant weight for oceanographers who model carbon cycling, because it suggests that mortality-driven carbon fluxes may be systematically misattributed in time if they are inferred solely from changes in cell abundance. Carbon could be flowing into microbial food webs and the deep ocean at moments when blooms appear to be thriving.

The methods developed by the Kyoto team for quantifying this invisible death of plankton offer a valuable new lens for understanding material flows within ecosystems. The researchers are careful to note the study’s limits. The reasons for plankton mortality are diverse, spanning grazing, nutrient starvation, disease and viral attack, and this study did not distinguish between different causes of cell lysis. The flux model detects death, but not its perpetrator. The team now intends to develop approaches that can track both the impacts and the causes of cell lysis at the species level, a step that would allow ecologists to attribute carbon release to specific pathogens and specific hosts within complex natural communities.

For Endo, the work is the continuation of a long-standing fascination with the viral dark matter of the sea. Since we revealed that a wide variety of viruses are present in seawater, I have been interested in understanding their impact on the ecosystem, he says. Using this research as a starting point, I hope to shed light on the true nature of the plankton ecosystem. As the technique matures and moves from laboratory cultures toward field applications, it could transform how scientists monitor ocean health, refine global carbon models, and appreciate the ceaseless, mostly invisible cycle of life and death playing out in every drop of seawater.

Subject of Research: Quantifying viral cell lysis of marine plankton using extracellular ribosomal RNA

Article Title: Dead or alive, plankton support marine ecosystems

Article References: Dead or alive, plankton support marine ecosystems. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: plankton, viral lysis, phytoplankton, rRNA, digital PCR, dissolved organic carbon, marine ecosystems, biogeochemical cycles, diatoms, raphidophytes, carbon sequestration, ocean viruses