A team of mycologists and microbial ecologists from Rovira i Virgili University in Reus, Spain, led by Alan Omar Granados-Casas, Alberto Miguel Stchigel, Ana Fernández-Bravo and José Francisco Cano-Lira, compared sediment communities from two strikingly different neighbouring water bodies. Salada Grande de Chiprana is a hypersaline lagoon whose waters are far saltier than the ocean, while the nearby La Estanca is an oligohaline lagoon with only low levels of dissolved salts. By sampling both, the researchers could ask a deceptively simple question: does salinity structure the invisible communities of fungi and prokaryotes that live in lagoon sediments, and how reliable are the molecular tools used to detect them?

The team used DNA metabarcoding, a technique that extracts environmental DNA from sediment, amplifies a specific genetic marker with the polymerase chain reaction, and then sequences the resulting mixture to identify which organisms are present. For fungi, the researchers targeted the internal transcribed spacer region of the nuclear ribosomal DNA, the standard barcode for fungal identification. Crucially, they ran two versions of this marker, ITS1 and ITS2, which flank the 5.8S ribosomal RNA gene and are often treated as interchangeable in the literature. For prokaryotes, meaning bacteria and archaea, they sequenced the 16S ribosomal RNA gene, the long-standing workhorse of bacterial diversity surveys.

When the two fungal marker datasets were analysed together, the fungal communities in both lagoons were dominated by three major lineages: the phylum Ascomycota, which contains most described fungal species; the Rozellomycota, a mysterious group of obligate parasites of other microorganisms; and the Basidiomycota, which includes mushrooms and their relatives. The prokaryotic assemblages, by contrast, were composed mainly of Pseudomonadota, a hugely diverse bacterial phylum, along with Cyanobacteriota, the photosynthetic bacteria that often form conspicuous microbial mats in saline environments, plus Bacteroidota and Chloroflexota, both common in sediments rich in organic matter.

The first surprise came from the diversity estimates themselves. When the researchers counted the number of distinct amplicon sequence variants, or ASVs, in each sample, they found no significant difference in fungal alpha diversity between the hypersaline and oligohaline lagoons. In other words, the saltier environment did not appear to host a depauperate fungal community compared with its brackish neighbour. However, the choice of marker mattered: the ITS2 primer pair recovered a significantly higher number of observed ASVs than ITS1, a difference the authors report as statistically significant with a p-value of 0.016. Two markers from the same genomic region, amplified from the same sediments, delivered measurably different inventories of fungal life.

The deeper analysis sharpened that warning. Using Bray-Curtis dissimilarity, a measure of how different community compositions are between samples, combined with PERMANOVA, a permutation-based statistical test for community data, the team found that fungal community composition was significantly associated with two factors: the identity of the lagoon and the molecular marker used. Remarkably, the marker choice explained more of the variation in the fungal data than the lagoon identity itself, and there was also a significant interaction between the two, meaning the apparent effect of the lagoon depended on which marker was being examined. For a field that often draws ecological conclusions from a single marker, that is a sobering result.

Salinity, the environmental variable most obviously differentiating the two lagoons, turned out to be a weaker predictor than expected. The researchers used electrical conductivity as a proxy for salinity and found that it explained only a limited and statistically non-significant fraction of the variation in fungal community composition. The authors are careful to note an important caveat: because the two lagoons differ in more ways than one, conductivity’s independent contribution could not be cleanly separated from other environmental differences between the sites. The hypersaline lagoon is not simply a saltier version of La Estanca; it is a distinct ecosystem with its own chemistry, hydrology and history, and any of those factors could be shaping its fungal residents.

The prokaryotic side of the story unfolded differently. While the bacterial and archaeal communities showed clear taxonomic differences between the two lagoons, the beta-diversity analysis found no statistically significant separation between them at the community level, largely because of substantial variability among samples taken within each lagoon. This contrast between fungi and prokaryotes is one of the study’s most intriguing findings. Two major branches of life, sampled from the same handful of sediments with standard molecular methods, responded in visibly different ways to the same environmental gradient. It suggests that fungal and prokaryotic communities are governed by different ecological rules in these systems, perhaps reflecting differences in dispersal ability, dormancy strategies, or the way each group partitions the sediment environment.

Perhaps the most tantalising result is what the researchers could not identify. A large fraction of the fungal ASVs recovered from the sediments remained taxonomically or functionally unclassified, meaning they did not match any known reference sequence well enough to assign a name or a role. These sediments, it appears, harbour poorly characterised fungal diversity, possibly including lineages new to science or at least new to databases. Inland hypersaline environments are understudied compared with marine and terrestrial habitats, and European examples in particular have rarely been surveyed for fungi with modern molecular methods. Chiprana’s sediments may therefore represent a reservoir of unknown fungal life adapted to some of the saltiest non-marine conditions on the continent.

The broader lesson of the study extends well into the booming world of environmental DNA research. Metabarcoding studies now underpin everything from biodiversity monitoring to climate impact assessments, and most rely on a single marker per organismal group. This work shows that for fungi, ITS1 and ITS2 are not interchangeable windows onto the same community: they recover complementary, partially overlapping views, and conclusions drawn from one may not survive scrutiny with the other. The authors argue that marker choice must be explicitly considered when interpreting metabarcoding-based ecological patterns, and that combining markers, as they did here, offers a more complete picture. For the microbial ecologists charting life in Earth’s extreme environments, the message is clear: before declaring what lives in a hypersaline lagoon, it pays to check which lens you are looking through.

Subject of Research: Fungal and prokaryotic sediment communities in hypersaline and oligohaline lagoons assessed by ITS and 16S rRNA metabarcoding

Article Title: Marker-Dependent Biases and Contrasting Fungal and Prokaryotic Community Patterns in Hypersaline and Oligohaline Lagoons

Article References: Marker-Dependent Biases and Contrasting Fungal and Prokaryotic Community Patterns in Hypersaline and Oligohaline Lagoons. (n.d.). https://doi.org/10.1007/s00248-026-02900-5

Image Credits: AI Generated

DOI: 10.1007/s00248-026-02900-5

Keywords: hypersaline lagoons, fungal ecology, metabarcoding, ITS1, ITS2, 16S rRNA, prokaryotes, salinity, Chiprana, microbial diversity, extremophiles, sediment microbiology

The research, led by Yuguang Wang, Longqi Xu and colleagues at Central South University in Changsha, China, examined a river system impacted by acid mine drainage, sampling both the flowing water and the underlying sediments along the contamination gradient. Rather than treating the microbial community as a single entity, the team split it into three compartments: the whole prokaryotic community, the abundant taxa that dominate biomass, and the rare taxa that linger at vanishingly low concentrations. This partitioning matters because ecologists have increasingly recognized that the rare biosphere, the enormous reservoir of low-abundance microorganisms, may behave according to entirely different rules than its abundant counterparts.

The first major finding concerns spatial structure. In sediment habitats, diversity and composition of the whole community and of abundant taxa changed significantly along the river, tracking the geochemical shifts imposed by the drainage. The relative abundances of Gammaproteobacteria and Betaproteobacteria, classes that often thrive in the most acidic, metal-rich zones near the pollution source, declined progressively downstream. In their place, Alphaproteobacteria and members of the phylum Acidobacteriota increased, suggesting a succession of acid-tolerant specialists as conditions gradually moderated. This directional turnover mirrors patterns documented in other acid mine drainage systems across southern China, where environmental heterogeneity and geographic isolation jointly sculpt microbial succession.

Water habitats told a strikingly different story. Unlike the sediments, the water column showed no significant spatial variation in community diversity or composition for the whole community or abundant taxa. Instead, the water was characterized by genera such as Acidovorax and Acidocella, acidophilic bacteria well adapted to the chemically uniform, continuously mixed conditions of the river channel. The contrast between sediment and water underscores a fundamental principle of microbial biogeography: habitat type can override pollution gradients in determining which ecological forces dominate. Sediments, with their layered chemistry, particle surfaces and pore waters, create microenvironments where deterministic filtering by environmental conditions leaves a clear spatial fingerprint. The well-mixed water column, by contrast, homogenizes conditions and appears to erase much of that spatial signal.

To understand how these communities came to be, the researchers turned to the conceptual machinery of community assembly theory. Ecologists distinguish between deterministic processes, in which environmental selection favors organisms with suitable traits, and stochastic processes, in which random dispersal, ecological drift and historical contingency shape which species end up where. Using null model analysis, which compares observed community turnover against what would be expected by chance, the team quantified the relative contributions of heterogeneous selection, homogeneous selection, dispersal limitation, dispersal and undominated processes.

The verdict was clear: stochasticity rules, especially for the rare biosphere. Dispersal limitation and undominated processes, a category capturing the combined effects of weak selection and weak dispersal, generally dominated community assembly, and this was most pronounced for rare taxa. The alpha diversity of rare taxa showed no significant correlation with spatial distance in either sediments or water, indicating that these low-abundance organisms are distributed in ways that defy simple geographic or environmental gradients. For the abundant taxa and the whole community in sediments, however, deterministic processes, both heterogeneous and homogeneous selection, still played a role that could not be ignored. In other words, the dominant players in the sediment are filtered by the harsh chemistry of acid mine drainage, while the rare players arrive and persist largely by chance.

Perhaps the most provocative result came from the co-occurrence network analysis. When the researchers mapped which taxa appear together across samples, constructing a network of potential ecological interactions, they found that rare taxa occupied important topological positions. These are the nodes that connect distant parts of the network, acting as potential keystone species whose removal could restructure the entire community. The finding resonates with a growing body of evidence that the rare biosphere punches far above its numerical weight. Studies in fertilized soils, acidic soils and other ecosystems have shown that rare microorganisms can be major drivers of ecosystem multifunctionality, and theoretical work has argued that the rare biosphere may serve as a dormant seed bank that resuscitates during pulses of ecosystem activity.

Why would rare taxa occupy such influential positions in a system as extreme as an acid mine drainage river? One possibility is that rarity itself is a strategy. Many rare organisms are specialists with narrow environmental tolerances, active only in fleeting favorable microenvironments. In a chemically heterogeneous system, these specialists may broker interactions between abundant generalists, facilitating the transfer of metabolites such as organic acids, iron species or sulfur intermediates across guild boundaries. Another possibility is that network edges involving rare taxa reflect shared responses to fine-scale environmental variation that abundant taxa, buffered by their sheer numbers, do not experience. Either way, the result challenges the practice of focusing monitoring and remediation assessments solely on dominant organisms.

The study also carries practical implications for managing mine-polluted rivers. Acid mine drainage is a global problem, contaminating thousands of kilometers of waterways with acidity, iron, aluminum, manganese and toxic metalloids. Natural attenuation, the gradual reduction of pollutant loads by intrinsic physical, chemical and biological processes, depends heavily on microbial activity, particularly sulfate-reducing bacteria and iron-cycling organisms that can immobilize metals as sulfides and oxides. If rare taxa hold key positions in the interaction networks that underpin these functions, then perturbations that further reduce rare diversity, such as episodic acid pulses or engineering interventions that disturb sediments, could have outsized and unpredictable consequences for the river’s capacity to heal itself.

The research also refines how scientists should read microbial communities as pollution indicators. Previous work on copper-contaminated river sediments suggested that abundant taxa are more sensitive bio-indicators than rare ones, and the present study partly supports that view: abundant taxa in sediments responded strongly and predictably to the spatial environmental gradient. But the new findings add nuance. Abundant taxa may tell you where the pollution is, while rare taxa may tell you how the ecosystem is wired. Effective ecological evaluation of acid mine drainage impact, the authors suggest, requires tracking both compartments and recognizing that they are assembled by different forces.

Methodologically, the study exemplifies the current toolkit of microbial ecology. High-throughput amplicon sequencing of the 16S ribosomal RNA gene, processed through rigorous quality control and denoising pipelines, provided the taxonomic inventory. Environmental variables measured alongside the biological samples allowed the team to link community patterns to geochemistry. Null models converted patterns into process, and network analysis converted co-occurrence into hypotheses about interaction. This integrated approach is rapidly becoming the standard for disentangling the ecology of complex microbial systems, from Antarctic lakes to tropical ocean waters to contaminated rivers.

The broader message is one of humility about where ecological power resides. In a river poisoned by acid mine drainage, the visible story, the dominant Gammaproteobacteria near the source, the Acidobacteriota downstream, the Acidovorax in the water, is written by environmental selection and reads clearly along the pollution gradient. But the hidden story, the one told by dispersal limitation, random drift and the quiet influence of organisms too scarce to notice, may be just as important. As the rare biosphere continues to reveal itself across ecosystems, ecologists are learning that in microbial worlds, less may indeed be more, and the smallest players may hold the strings of the entire system.

Subject of Research: Microbial community assembly of abundant and rare prokaryotic taxa in an acid mine drainage-impacted river system

Article Title: Distinct ecological patterns of abundant and rare prokaryotic taxa across sediment and water habitats in an acid mine drainage-impacted river system

Article References: Wang, Y., Xu, L., Ai, C., Chen, Z., Zhou, H., & Cheng, H. (2026). Distinct ecological patterns of abundant and rare prokaryotic taxa across sediment and water habitats in an acid mine drainage-impacted river system. Environmental Geochemistry and Health, 48(15), Article 619. https://doi.org/10.1007/s10653-026-03523-y

Image Credits: AI Generated

DOI: 10.1007/s10653-026-03523-y

Keywords: acid mine drainage, rare biosphere, microbial ecology, community assembly, co-occurrence network, prokaryotes, sediment microbiology, river pollution, heavy metals, stochastic processes, biogeography, environmental microbiology

The research was led by Dr. Meng Li of the Institute for Advanced Study at Shenzhen University, working with colleagues across six national nature reserves that protect seven representative mangrove wetlands along the Chinese coast. In total, the team collected 300 sediment samples, a sampling intensity that allowed them to compare fungal assemblages both among distant wetlands and within individual sites. Mangrove wetlands are among the most demanding habitats on Earth for microbial life. They sit at the tropical and subtropical land-sea interface, where sediments experience high salinity, low oxygen availability, and an abundance of organic matter, conditions that together create a powerful environmental filter for any organism attempting to persist there.

Fungi matter enormously in these systems. They are among the few organisms capable of efficiently decomposing lignocellulose, the tough structural material of plant tissues, and their activity drives much of the nutrient cycling that sustains mangrove food webs. Despite this ecological importance, the diversity, biogeographic distribution, and assembly mechanisms of sediment fungal communities in mangroves had remained poorly characterized, a gap the new study set out to close with a combination of high-throughput sequencing and ecological modeling.

Methodologically, the team employed dual-amplicon high-throughput sequencing, simultaneously targeting the fungal internal transcribed spacer 2 region and the prokaryotic 16S rRNA gene. This design allowed fungal and prokaryotic communities to be characterized from the same samples, opening the door to direct analysis of cross-kingdom relationships. The sequencing effort recovered 14,771 fungal operational taxonomic units, distributed across 15 phyla, 51 classes, and 594 genera. Perhaps the most humbling number in the dataset is this: roughly one-third of the observed fungal diversity could not be assigned to any known phylum. Mangrove sediments, it turns out, harbor a substantial reservoir of fungi that are effectively unknown to science, lineages whose ecological roles remain entirely unexplored.

The survey also highlighted the prominence of early-diverging fungal lineages. Rozellomycota and Chytridiomycota, groups that branch near the base of the fungal tree of life, proved to be relatively diverse and widely distributed across the sampled wetlands. Their prevalence in these sediments suggests that mangrove ecosystems may serve as important refugia for ancient fungal lineages, and it underscores how much of fungal evolutionary history remains concentrated in environments that have historically been undersampled by mycologists, who have traditionally focused on soils, forests, and freshwater systems.

When the researchers examined biogeographic patterns, a clear hierarchy of influences emerged. Geographic location exerted a stronger effect on fungal community composition than the identity of the mangrove plants themselves. Fungal communities clustered primarily by sampling site rather than by vegetation type, and two factors were associated with these patterns: mean annual temperature and dispersal limitation. The explanation likely lies in the fragmented geography of mangrove forests themselves. Because mangroves occur in patchy stands separated by stretches of unsuitable coastline, long-distance dispersal of fungal propagules between wetlands is restricted. Each forest effectively functions as a partially isolated microbial island, allowing communities to diverge over time through the combined action of environmental sorting and limited gene flow.

Zooming in to the local scale, the picture changes. Within individual wetlands, salinity and the carbon-to-nitrogen ratio emerged as the main environmental factors associated with variation in fungal community structure. Salinity acts as a physiological gatekeeper: high salt concentrations limit fungal growth to taxa capable of tolerating osmotic stress, filtering out sensitive lineages and favoring halotolerant specialists. The carbon-to-nitrogen ratio reflects the balance between carbon availability and nitrogen supply in the sediment. When this ratio is elevated, it signals an imbalance that may constrain which taxa can persist, because decomposer fungi require nitrogen to build the enzymes that break down carbon-rich plant litter. Intriguingly, total phosphorus showed an indirect positive association with fungal diversity, likely operating through its influence on nutrient availability and on the connectivity of the microbial co-occurrence network, rather than through any direct effect on fungal physiology.

To probe these biotic interactions, the team constructed a co-occurrence network from the most abundant fungal and prokaryotic taxa. The resulting network contained 777 nodes and 3,680 edges, and a remarkable 99 percent of those edges represented positive correlations, suggesting that coexistence and cooperation, rather than exclusion, dominate the visible structure of the mangrove sediment microbiome. Bacteria and archaea exhibited higher average connectivity than fungi and formed the structural backbone of the network. Yet certain fungal nodes occupied central positions, acting as potential bridges that link fungal and prokaryotic components of the community. These hub fungi may represent keystone taxa whose activities, perhaps through the decomposition of complex organic matter, create resources and conditions that shape the surrounding microbial neighborhood.

The analytical centerpiece of the study is a piecewise structural equation model, a statistical framework that allows researchers to test networks of hypothesized causal pathways rather than isolated correlations. Using this approach, the authors integrated their results into a three-tier model of fungal community assembly. At the regional scale, temperature and dispersal limitation filter which lineages can reach and survive in a given wetland. At the local scale, salinity and nutrient conditions, including the carbon-to-nitrogen ratio and phosphorus availability, further sort the regional species pool. At the micro scale, cross-kingdom interactions with bacteria and archaea fine-tune community structure. No single factor explains who lives in the mud; instead, nested layers of environmental and biological filtering operate simultaneously across spatial scales.

The implications extend beyond basic mycology. Mangrove wetlands are under sustained pressure from coastal development, sea-level rise, and changing salinity regimes, and the microbial communities that power their nutrient cycles will respond to these changes in ways that are only beginning to be understood. By establishing that salinity and nutrient chemistry govern local fungal assemblages while temperature and dispersal shape regional patterns, the study provides a predictive framework for anticipating how sediment fungal communities might shift as coastal environments warm and saltwater intrusion intensifies. Just as importantly, the large fraction of unclassified fungal diversity signals that a vast amount of functional novelty remains hidden in these sediments, potentially including enzymes relevant to lignocellulose degradation and other biotechnological applications. For now, the muddy forests of the Chinese coast have offered a rare, scale-resolved glimpse of the hidden fungal architecture beneath one of the planet’s most productive ecosystems, and that architecture turns out to be built layer by layer, from the regional climate down to the microscopic handshakes between species.

Subject of Research: Scale-dependent assembly and biogeography of fungal communities in Chinese mangrove sediments

Article Title: Chinese mangrove sediments reveal scale-dependent assembly of fungal communities

Article References: Chinese mangrove sediments reveal scale-dependent assembly of fungal communities. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: mangrove, fungal communities, sediment microbiology, biogeography, dispersal limitation, salinity, carbon-to-nitrogen ratio, co-occurrence network, structural equation modeling, Rozellomycota, Chytridiomycota, high-throughput sequencing