The research, published in the journal Biogeosciences, was carried out at the Leipzig Canopy Crane, a research facility operated by the German Centre for Integrative Biodiversity Research (iDiv) in one of the largest remaining floodplain hardwood forests in Central Europe. The site, located in the floodplain of the Elster, Pleiße, and Luppe rivers near Leipzig, Germany, is dominated by sycamore maple, common ash, English oak, and hornbeam, and hosts a continental climate with an annual mean temperature of 9.7 degrees Celsius. From March 2019 to February 2020, a team of researchers led by Ettore Fedele of Leipzig University and Swansea University, together with colleagues from Justus Liebig University Giessen and iDiv, collected passive air samples every week at three different heights above the forest floor: 3, 15, and 28 meters. Nine Durham-type spore traps, each fitted with a sterile Petri dish coated in a thin layer of Vaseline, were deployed across three sampling stations separated by 40 to 60 meters, capturing whatever fungal material the air delivered.

Rather than relying on microscopy, which can identify only a fraction of airborne fungi, the team turned to DNA metabarcoding of the fungal internal transcribed spacer (ITS) region, a genetic barcode widely used to distinguish fungal species. DNA was extracted from the collected samples, amplified with three different primer combinations chosen to maximize taxonomic coverage, and sequenced on an Illumina MiSeq platform. The resulting reads were processed with the DADA2 pipeline, which infers exact amplicon sequence variants with single-nucleotide resolution, and taxa were assigned using the IDTAXA classifier against the UNITE database, supplemented by BLASTN searches against the NCBI reference database. After quality filtering and removal of contaminants and low-abundance variants, the final dataset comprised more than 1.4 million fungal sequencing reads and 760 distinct sequence variants, providing an unusually rich census of the forest’s aerial mycobiome.

The results paint a clear taxonomic picture. Ascomycota, the most species-rich fungal phylum, dominated the airborne community with 74.3 percent of all reads, followed by Basidiomycota at 25.1 percent, with all remaining phyla together accounting for less than one percent. Three genera stood out as the consistent workhorses of the air: Cladosporium, which alone made up 30.52 percent of total reads, Epicoccum at 11.58 percent, and Alternaria at 5.62 percent. All three belong to the class Dothideomycetes and are familiar names in aerobiology, not least because they rank among the best-known triggers of allergic reactions and plant diseases worldwide. Their dominance in the Leipzig air mirrors patterns reported from other temperate environments, from Havana to Salamanca to Bratislava, underscoring how consistent the major players in the airborne fungal world are across regions.

The study’s central finding concerns temperature. When the researchers compared community composition across the twelve monthly sampling periods using permutational multivariate analysis of variance, average air temperature emerged as the only meteorological variable significantly correlated with shifts in the fungal aerosol community. Neither humidity, which ranged from 50.3 percent in June to 84.3 percent in December, nor rainfall, nor wind speed showed significant associations. When the team split the year into warm and cold months around the study period’s mean temperature of 13.29 degrees Celsius, a striking pattern emerged: Ascomycota became significantly more abundant during warmer months, while Basidiomycota dominated the colder ones. Wilcoxon rank-sum tests confirmed both differences were highly significant. The three dominant genera all peaked in summer, with Cladosporium reaching its maximum in July and Epicoccum and Alternaria in August, while the basidiomycete yeasts Vishniacozyma and Itersonilia peaked in January, the coldest month of the study.

Digging deeper with differential abundance analysis, the researchers identified 68 sequence variants belonging to 66 different genera, roughly 21 percent of the genera analyzed, whose abundance shifted significantly with seasonal temperature. Nearly 40 percent of Ascomycota genera responded positively to warmer conditions, whereas only 15 percent of Basidiomycota genera did so. Among the temperature-responsive taxa were several of considerable practical concern. The genus Erysiphe showed the strongest positive response to warming, and one variant was identified as Erysiphe alphitoides, the invasive pathogen responsible for oak powdery mildew, a disease that poses a significant threat to forest health and productivity across Europe. The dataset also contained Zymoseptoria tritici, a major pathogen of wheat, suggesting that nearby agricultural areas contribute fungal propagules to the forest air. On the allergen front, the summer peaks of Cladosporium and Alternaria, both potent respiratory allergens linked to asthma exacerbations, align with earlier work connecting these genera to high temperatures and low humidity.

One of the study’s more surprising results was what it did not find: any meaningful vertical structure in the fungal community. Despite sampling at heights spanning 25 meters, from near the ground to the upper canopy, neither trap height nor sampling location had a significant effect on fungal diversity, and height explained only a trivial two percent of the variation in community composition. The researchers attribute this to the continuous turbulent mixing of air within the planetary boundary layer, the lowest part of the atmosphere, which effectively homogenizes airborne particles across altitudes below the canopy top. Backward air-mass trajectory modeling using the HYSPLIT system confirmed that air arriving at the three sampling heights followed substantially overlapping paths, indicating that the fungi collected at different elevations originated from the same regional sources. This finding contrasts with studies in the Amazon rainforest, where bioaerosol concentrations declined markedly from understory to above the canopy, and highlights how boundary-layer dynamics can override the vertical stratification of source communities on the forest floor.

The team also defined a core mycobiome for the site: 27 sequence variants that appeared in every single sample collected throughout the year, representing the constant airborne fungal background of the Leipzig floodplain forest. At the class level, this core community was composed of Dothideomycetes, Tremellomycetes, Agaricomycetes, and Leotiomycetes, drawing members from both major fungal phyla. Establishing such a baseline matters, the authors argue, because knowing the stable background community makes it easier to identify local sources of bioaerosols and to separate their signal from the effects of external drivers such as weather and climate. Interestingly, the dataset also included taxa previously reported mainly outside Europe, such as Alanphillipsia aloetica, originally described from South Africa, a reminder that airborne fungal communities are shaped by long-distance dispersal as well as local sources.

The implications extend well beyond one forest. Because bioaerosols make up more than ten percent of atmospheric particulate matter, influence cloud formation and the hydrological cycle, and serve as sensitive indicators of ecosystem change, understanding what controls their composition is essential for predicting how ecosystems and human health will fare under climate change. The temperature-driven patterns documented here suggest that as summers warm, allergenic and pathogenic ascomycetes may become increasingly prominent in the air we breathe, with consequences for respiratory health, crop disease pressure, and forest management costs. The authors caution, however, that temperature effects on aerosol dynamics are entangled with temperature effects on the phenology of the source species themselves, making it difficult to disentangle direct influences on spore release from indirect effects mediated through fungal life cycles and host plant development.

For that reason, the researchers emphasize that a single year, however intensively sampled, is only a beginning. They call for multi-year monitoring with higher temporal resolution, potentially separating daytime and nighttime periods to capture the influence of diel temperature fluctuations, boundary-layer dynamics, and spore-release phenology. Such extended records would allow scientists to determine whether the temperature-mediated shifts in fungal abundance and composition observed at Leipzig persist or intensify under continuing climate change and increasingly frequent extreme events. In the meantime, the study stands as the first comprehensive assessment of meteorological influences on airborne fungi across seasonal cycles in a Central European floodplain forest, and as a benchmark against which future changes in the air’s invisible fungal cargo can be measured. The raw sequencing data have been deposited in the European Nucleotide Archive, ensuring that this aerial census of a hidden world remains open to the researchers who will build upon it.

Subject of Research: Seasonal dynamics of airborne fungal communities in a temperate floodplain forest assessed by DNA metabarcoding

Article Title: Unlocking the air: DNA metabarcoding sheds light on seasonal fungal dynamics in a temperate floodplain forest

Article References: Fedele, E., Müller, C. M., Wissemann, V., Gemeinholzer, B., Wirth, C., & Sánchez-Parra, B. (2026). Unlocking the air: DNA metabarcoding sheds light on seasonal fungal dynamics in a temperate floodplain forest. Biogeosciences, 23(19), 6931-6945. https://doi.org/10.5194/bg-23-6931-2026

Image Credits: AI Generated

DOI: 10.5194/bg-23-6931-2026

Keywords: airborne fungi, DNA metabarcoding, bioaerosols, floodplain forest, seasonal dynamics, temperature, Ascomycota, Basidiomycota, Cladosporium, allergens, plant pathogens, climate change

The team assembled 128 miniature grassland communities in pots at the University of Alicante, each containing four individuals drawn from sixteen common European grassland species. Eight were grasses, including meadow fescue, perennial ryegrass, and timothy; eight were forbs, the broad-leaved wildflowers of the meadow, including yarrow, daisy, ribwort plantain, and dandelion. By varying the proportion of grasses from zero to one hundred percent, the researchers created a gradient of functional diversity, a coarse but informative proxy for how differently the species in each pot made their living. Half the pots received living inoculum of four AMF species commonly found in European grasslands, cultured at Agroscope’s Swiss Collection of Arbuscular Mycorrhizal Fungi; the other half received the same inoculum after sterilization. Every pot also received a microbial filtrate to equalize the background soil community, isolating the effect of the fungi themselves.

Then came the twist that reshaped the entire study. When the researchers checked their controls, they found that the supposedly fungus-free pots were anything but. Root colonization averaged 53 percent in sterilized controls versus 61 percent in inoculated pots, and the proportion of AMF DNA reads among all fungal sequences was essentially identical in both treatments. Airborne spores, incomplete substrate sterilization, or fungal propagules hitchhiking on surface-sterilized seeds most likely seeded the control pots. A truly AMF-free control, the authors concluded, was unattainable, which is arguably more realistic: in nature, soils are never fungus-free, and plants always respond against a backdrop of resident mycorrhizal communities.

Rather than scrapping the experiment, the team pivoted. DNA extracted from the soils of 96 pots was amplified with fungal ITS2 primers and sequenced on an Illumina NovaSeq platform, yielding nearly 5.7 million quality-filtered reads. After clustering at 97 percent identity and screening against the UNITE and FungalTraits databases, the researchers identified 233 AMF operational taxonomic units among 6355 fungal OTUs. Crucially, the living inoculum had not simply added fungi; it had restructured the community. Rarefied AMF richness was significantly lower in inoculated pots, apparently because the four introduced strains, known competitors such as Rhizoglomus and Claroideoglomus, monopolized root and soil niches and excluded the background taxa. Inoculation had inadvertently created a gradient of fungal diversity rather than a simple presence-versus-absence contrast.

That gradient told an unexpected story. Contrary to the complementarity hypothesis, which predicts that diverse fungal communities should boost plant productivity through differentiated resource uptake, biomass production declined as AMF richness rose. Root biomass showed the clearest signal, decreasing significantly with fungal richness regardless of the grass proportion in the community. Aboveground production also fell with richness, though the effect was weaker and moderated by community composition. The most productive communities were grass-dominated pots carrying the engineered low-diversity inoculum, a result that directly contradicts the expectation that diversity begets function at every level of the soil food web.

The explanation the authors favor is one of dominance rather than diversity. Fungal taxa differ enormously in how effectively they deliver nutrients to their hosts, and the four inoculated species are among the best-documented performers in the literature. By concentrating the community around a few highly functional, highly competitive strains, inoculation produced more biomass per plant even as it squeezed out the broader fungal repertoire. In other words, a few excellent traders beat a large crowd of mediocre ones, at least for total biomass. This mechanism echoes findings from agricultural soils, where competitive inoculant strains can lift crop yields while eroding the indigenous mycorrhizal diversity that underpins long-term ecosystem resilience.

Yet the biomass ledger concealed a deeper asymmetry between plant types. When the researchers examined how the response to fungal richness varied with grass dominance, a pattern emerged: the negative effect of fungal richness on leaf production weakened as the proportion of forbs increased. Communities dominated by forbs benefited more from a diverse AMF community than grass-dominated ones, which thrived instead under the low-diversity inoculum. Although this interaction was statistically marginal, the authors attribute it to fundamental differences in resource economy. Grasses, with their fast growth and fine root architecture, are often less dependent on mycorrhizal supply, whereas many forbs, particularly non-nitrogen-fixing species with higher carbon demands from multiple symbioses, rely more heavily on fungal partners and may profit from a wider menu of fungal strategies.

The study also revealed a striking division of labor between the aboveground and belowground worlds. Aboveground biomass was governed primarily by plant functional composition: grass-dominated communities produced the most shoot material, likely because grasses’ upright growth form allows them to escape competition for light, while forbs with broad horizontal leaves shade more easily. Belowground biomass, by contrast, was governed primarily by fungal diversity, with almost no influence of plant composition. This split suggests that AMF act chiefly through root-mediated resource acquisition and allocation, a finding consistent with recent large-scale evidence that mycorrhizal symbiosis enhances soil carbon storage by pushing biomass investment underground. The hyphal networks that flourish under such investment may in turn improve soil structure, water retention, and nutrient availability for the whole community.

For the booming industry in commercial mycorrhizal biofertilizers, the implications are sobering. Inoculants are increasingly marketed as a green alternative to chemical fertilizers, and they can indeed raise yields. But this experiment demonstrates that adding fungi is not the same as adding fungal diversity, and that the two can move in opposite directions. A commercial treatment that concentrates the community around a few productive strains may boost short-term biomass in grass-dominated systems while sacrificing the native diversity that forb-rich, biodiverse grasslands depend on. The authors argue that sustainable land management requires understanding the specific interactions between plant functional groups and fungal community composition, not simply dosing soils with spores.

The broader lesson is that the relationship between biodiversity and ecosystem function, one of ecology’s most celebrated patterns, is not a simple staircase. Context matters at every scale: which plants are present, which fungi are present, and how their resource economies match. By coupling DNA-based assessments of fungal richness with experimental gradients of plant functional diversity, this study offers a template for disentangling those mechanisms in semi-arid grasslands and beyond. The next step, the authors suggest, is to extend the joint assessment of plant and fungal functional diversity to ecosystem processes such as nutrient cycling, where their models already hinted at treatment-dependent shifts in soil nitrogen and phosphorus availability. In the hidden economy beneath our feet, it seems, diversity is currency, but who gets rich depends entirely on who is trading.

Subject of Research: Effects of arbuscular mycorrhizal fungal diversity and plant functional composition on biomass production in semi-arid grassland communities

Article Title: Forb species benefit more than grasses from a diverse arbuscular mycorrhizal fungal community in semi-arid grasslands

Article References: Shpilkina, Y., Vasar, M., Asensio, S., Ochoa, V., Gozalo, B., Enste, K., Zobel, M., de Bello, F., van der Heijden, M., Maestre, F. T., & Neuenkamp, L. (2026). Forb species benefit more than grasses from a diverse arbuscular mycorrhizal fungal community in semi-arid grasslands. Web Ecology, 26(2), 119-155. https://doi.org/10.5194/we-26-119-2026

Image Credits: AI Generated

DOI: 10.5194/we-26-119-2026

Keywords: arbuscular mycorrhizal fungi, soil biodiversity, grasslands, forbs, grasses, plant functional diversity, biomass production, fungal inoculants, root colonization, DNA metabarcoding, semi-arid ecosystems, sustainable agriculture

The study, led by Lorenzo Zacchetti of the National Research Council’s Institute for Biological Resources and Marine Biotechnologies in Ancona, together with colleagues from the University of Bologna, the National Biodiversity Future Center, the CNR Institute of Research on Terrestrial Ecosystems and Liverpool John Moores University, introduces what the authors call the Gut-Isotope-DNA, or GID, approach. According to the researchers, this is the first time such an integrated framework has been applied to a crustacean. The method weaves together three techniques that each carry different strengths and blind spots: gut content analysis, which identifies prey visually but only captures recently ingested and recognisable items; stable isotope analysis, which integrates diet over weeks to months but resolves prey only at broad categories; and DNA metabarcoding, which can detect even soft, digested or unrecognisable prey from trace genetic material.

The fieldwork took place in one of the most intriguing features of the Adriatic basin: the Pomo Pits, two deep depressions in the middle of the sea that host a legally protected Fishery Restricted Area. Specimens of Norway lobster were collected both inside and outside this protected zone during two separate surveys, in 2019 and 2023, giving the team a rare opportunity to test whether diet and gut microbiome differ between a heavily fished area and a refuge, and whether these patterns shift between years separated by a four-year gap. The samples were gathered during scientific trawl surveys funded by the Italian Ministry of Agricultural, Food, and Forestry Policies in 2019 and by the European H2020 NAUTILOS project in 2023, which was designed to validate new low-cost ocean observation instruments on fishing vessels.

When the researchers opened up the lobsters’ guts and examined the contents under the microscope, one prey species towered above all others: the squat lobster Iridonida speciosa, a small relative of the Norway lobster that shares the same muddy habitat. This visual finding was not a fluke of preservation. Stable isotope mixing models, which use the ratios of carbon and nitrogen isotopes in the predator’s tissues to estimate the proportions of different food sources, independently pointed to the same conclusion. Together, the two methods painted a picture of an animal whose diet is anchored on a single abundant resource, at least in the parts of its menu that are large and durable enough to survive digestion intact.

But the DNA metabarcoding results told a richer and more nuanced story. By amplifying and sequencing genetic markers from the gut contents, the team detected a much wider array of prey than visual inspection had revealed, including soft-bodied organisms and fragments that would never survive to be identified under a dissection microscope. The molecular data exposed the Norway lobster as a genuine mixed scavenger-predator, opportunistically consuming both live prey and carrion across the seafloor. Intriguingly, the dietary diversity recorded through metabarcoding was higher in 2019 than in 2023, and finfish contributed more to the diet in the earlier year. This temporal pattern held both inside and outside the Pomo Pits, suggesting that shifts in food availability or feeding behaviour between the two survey years rippled through the population regardless of protection status.

The most striking twist came from the gut microbiome. Sequencing the bacterial communities living inside the lobsters’ digestive tracts revealed a microbial world dominated by three families: Vibrionaceae, a group of marine bacteria that includes both harmless associates and notable pathogens; Erysipelotrichaceae; and Mycoplasmataceae, cell-wall-less bacteria frequently found in the guts of crustaceans and other animals. These microbial residents were not passive bystanders. Their composition tracked the lobsters’ trophic patterns closely, with specimens caught outside the Pomo Pits carrying significantly more diverse gut microbial communities than those from inside the protected area.

What surprised the team most was the discriminating power of the microbiome itself. When the researchers asked which data stream best separated lobsters by sampling area and by year, the gut microbial communities outperformed the strictly dietary analyses. In other words, the invisible ecosystem within the gut acted as a sensitive recorder of where and when an animal lived and fed, sometimes more sharply than the food remains it carried. This finding raises the tantalising prospect that gut microbiomes could serve as biological indicators of habitat use and environmental conditions in commercially exploited species, complementing conventional tools such as stomach content analysis and population genetics.

The study also carries a methodological caution that the authors are careful to underline. While dietary composition and gut microbiome structure in the Norway lobster appeared broadly consistent with one another, each of the three techniques in the GID approach homes in on a different biological phenomenon. Gut content analysis captures a snapshot of recent, identifiable meals. Stable isotopes integrate assimilated diet over longer timescales but blur fine taxonomic detail. DNA metabarcoding maximises taxonomic resolution and detects trace prey but can be influenced by digestion rates, primer bias and the differential survival of DNA across prey types. Integrating evidence from all three therefore requires tailored interpretations, the researchers argue, and careful consideration of what each line of evidence can and cannot support, particularly when conclusions feed into fisheries management decisions.

That management dimension is far from academic. Nephrops norvegicus, known on dinner plates as scampi or langoustine, is one of the most economically important shellfish resources in European waters, and its stocks are assessed and regulated through effort controls, minimum landing sizes and area closures such as the Pomo Pits Fishery Restricted Area. Understanding what the species eats, where it forages and how its feeding ecology responds to protection and to environmental change is central to building sustainable management plans. If the lobster’s diet shifts between years, as the 2019 to 2023 comparison suggests, then trophic models underpinning stock assessments may need to account for that variability rather than assuming a static food web.

The GID framework, its developers suggest, could now be extended beyond a single species. Any crustacean, fish or benthic invertebrate whose diet is hard to observe directly could be profiled with the same triple lens, and the microbiome component adds a layer of ecological information that traditional diet studies simply do not capture. As sequencing costs continue to fall and reference databases of prey DNA grow, the approach may become a routine instrument in the marine ecologist’s toolkit. For now, the humble Norway lobster has become the first crustacean to have its meals, its chemistry and its inner microbial world read together, and the reading suggests an animal far more flexible, opportunistic and microbially distinctive than its muddy burrow home would ever let on.

Subject of Research: Dietary ecology and gut microbiome of the Norway lobster assessed through an integrated gut content, stable isotope and DNA metabarcoding approach

Article Title: Integrating Dietary Characterisation and Gut Microbiome Analysis in Norway Lobster (Nephrops norvegicus) Through Gut-Isotope-DNA (GID) Approach

Article References: Zacchetti, L., Basili, M., Domenichetti, F., Quero, G. M., Lauteri, M., Mariani, S., Manini, E., & Martinelli, M. (2026). Integrating Dietary Characterisation and Gut Microbiome Analysis in Norway Lobster (Nephrops norvegicus) Through Gut-Isotope-DNA (GID) Approach. Microbial Ecology. https://doi.org/10.1007/s00248-026-02902-3

Image Credits: AI Generated

DOI: 10.1007/s00248-026-02902-3

Keywords: Norway lobster, Nephrops norvegicus, gut microbiome, DNA metabarcoding, stable isotopes, trophic ecology, Adriatic Sea, Pomo Pits, fisheries management, Vibrionaceae, food web, marine ecology

The scale of the compiled dataset is striking. Across ten states and two union territories, the synthesis documented 205 soil faunal species and orders, distributed across three broad groups defined by the Food and Agriculture Organisation’s classification framework. Microfauna, including bacteria, fungi and protozoa, accounted for 47 recorded taxa, mesofauna such as mites, springtails and enchytraeids contributed 56, and macrofauna, encompassing earthworms, ants, termites and beetles, dominated with 102 species or orders. These organisms were recorded across 11 agricultural and tree-based land uses, spanning rice fields, organic farms, shifting cultivation, fallows, and plantations of teak, bamboo, acacia, cassia, mango and sal.

Geographically, the picture is deeply uneven. Karnataka emerged as the species-richest state with 53 recorded taxa, followed closely by Meghalaya with 49 and Tripura with 28, while Uttar Pradesh yielded only two species in the compiled literature. When the researchers calculated the Shannon-Wiener diversity index, a standard ecological metric that combines species richness with the evenness of their abundances, values ranged from a low of 0.3 in Uttar Pradesh to a high of 3.8 in Meghalaya. Intermediate values between 1.5 and 2.0 characterised Tripura, Orissa and Rajasthan, while Maharashtra, West Bengal, Tamil Nadu, and the union territory of Leh and Ladakh fell between 2 and 3. Meghalaya also recorded the highest number of mesofauna species, whereas Karnataka led in microfauna with 40 species.

The relationship between soil type and soil life proved equally revealing. Tripura and Tamil Nadu stood out with 20 soil faunal groups recorded across six soil types or orders, indicating diverse pedo-environmental conditions that support a wide range of below-ground communities. By contrast, the synthesis detected a weaker association between faunal diversity and soil type in Leh and Ladakh, Meghalaya and Rajasthan, a pattern the authors attribute to variation in pedo-climatic conditions. Across the national dataset, Inceptisols and sandy loam soils consistently supported the greatest diversity of ants, earthworms and microarthropods, particularly the springtails of the order Collembola and the mites of the group Cryptostigmata. The recurrence of earthworm genera such as Metaphire, Drawida and Perionyx across different soil types points to their broad ecological adaptation.

Land management emerged as a decisive filter on which organisms thrive. Croplands under conventional farming, with high inputs of inorganic fertilisers and pesticides, supported lower soil faunal diversity and abundance than ecologically managed systems. Microfauna and macrofauna, including earthworms, mites and springtails, were consistently present in organic and integrated farming systems, while conventional and integrated farms shared similar communities dominated by resilient taxa. Tree-based systems told their own story: the phylum Arthropoda was abundant in bamboo and teak plantations, suggesting favourable microclimatic conditions for detritivores and predators, and arthropod dominance was greater in the structured, litter-rich habitats under acacia, cassia, mango and sal than in agriculture, fallows or shifting cultivation. Actinomycetes appeared only under acacia plantations, possibly reflecting associations with litter or humus-rich soil, while millipedes and molluscs were found exclusively in mixed plantations.

To formalise these patterns, the team applied principal component analysis and Pearson correlation statistics in R. The PCA showed that the first two components together explained roughly half of the variability in faunal occurrence across agroecosystems, with PC1 accounting for 28 percent and PC2 for 22.2 percent. Most agroecosystems, including organic farming, shifting cultivation, acacia plantations and conventional agriculture, clustered together, indicating broadly similar soil faunal composition. But two systems stood apart: mixed plantations and mango orchards harboured unique, divergent communities. The mango orchard was particularly distant along PC1, its separation driven by ants, beetles, spiders, snails, centipedes and caterpillars, which correlated strongly and positively with that land use. In the correlation matrix, isolates and mesofauna showed an almost perfect positive relationship at r = 0.98, while species richness was negatively correlated with both mesofauna, at r = -0.17, and isolates, at r = -0.28, a counterintuitive result that underscores how little is still understood about the drivers structuring these communities.

The review places these findings against a sobering national backdrop. Soil degradation affects nearly 121 million hectares, roughly 40 percent of India’s land, and the average soil organic carbon content of Indian soils is about 0.54 percent, well below critical thresholds for biological function. Excessive inorganic fertiliser use induces acidification and disrupts the relationship between above-ground and below-ground biodiversity. The authors note that the diversity and abundance of soil organisms decline as soil organic carbon falls, reducing metabolic interactions, and they argue that India’s soil organic carbon management programmes and policies need reform. National schemes such as the National Mission for Sustainable Agriculture and the Soil Health Card programme currently focus on chemical fertility, leaving the biological dimension of soil health largely unmeasured at the national scale.

Climate change adds a further layer of urgency. The review highlights that rising temperatures accelerate microbial metabolism but can reduce diversity by favouring heat-tolerant species, while precipitation anomalies, producing droughts and floods, negatively affect microbial and faunal communities through shifts in soil moisture regimes. The higher diversity observed in Meghalaya and Karnataka suggests that moisture availability is critical for sustaining soil biota. The authors argue that the crop-climate-soil-biodiversity nexus must be understood across India’s diverse cropping systems and integrated with projected climatic scenarios, particularly since extreme weather events disproportionately harm sensitive or endemic taxa. They also flag a methodological gap: most Indian studies rely on a single sampling event, which limits any understanding of temporal change, and functional roles of soil organisms, assessed with tools such as metagenomics and meta-transcriptomics, remain scanty.

The path forward, the researchers conclude, lies in aligning Indian soil biodiversity science with international frameworks. They recommend adopting the standardised sampling protocols of the Global Soil Biodiversity Atlas and the Global Soil Biodiversity Initiative, deploying DNA metabarcoding for accurate estimates of microbial and faunal diversity, and developing agro-ecological zone-wise predictive models to anticipate the impacts of land-use change. They also call for research into soil microbial genomics, micro-food webs and the ecosystem services delivered by soil biota, arguing that soil biodiversity should be treated as a primary component of nature-based solutions for sustainable agriculture. With India’s 20 agro-ecological zones and 15 climatic zones harbouring an extraordinary but poorly documented wealth of underground life, the review makes clear that the country’s next agricultural revolution may depend less on what is planted above ground than on what is protected below it.

Subject of Research: Soil biodiversity research across Indian agroecosystems

Article Title: Mapping the progress of soil biodiversity studies in India to address research gaps and opportunities

Article References: Singh, M., Purohit, S., Wadhu, A. M., Hande, O. M., Khan, Y. D. I., & Gholkar, M. D. (2026). Mapping the progress of soil biodiversity studies in India to address research gaps and opportunities. Discover Soil, 3(1), Article 111. https://doi.org/10.1007/s44378-026-00260-7

Image Credits: AI Generated

DOI: 10.1007/s44378-026-00260-7

Keywords: soil biodiversity, India, agroecosystems, soil fauna, earthworms, microarthropods, Shannon-Wiener index, soil organic carbon, agroforestry, climate change, DNA metabarcoding, sustainable agriculture

The core challenge the researchers set out to solve is a familiar one to anyone working with trace biological evidence: DNA at crime scenes, in processed foods, or in seized wildlife products is rarely pristine. Heat, chemicals, time, and environmental exposure all shred the long DNA molecules that standard analytical methods depend on. Traditional DNA barcoding, which relies on amplifying a single gene region of several hundred base pairs, often fails outright when the template DNA is broken into pieces shorter than the target. The new assay sidesteps this limitation by targeting four mitochondrial genes simultaneously: cytochrome b (Cytb), cytochrome c oxidase subunit I (COI), 16S ribosomal RNA, and 12S ribosomal RNA. Because each of these markers can be amplified as short fragments, the probability that at least one usable stretch of DNA survives in a degraded sample rises dramatically.

Mitochondrial DNA is the molecule of choice for species identification for good reason. Each cell contains hundreds to thousands of mitochondrial copies compared with just two copies of any nuclear gene, which means mitochondrial targets are far more likely to yield amplifiable material from tiny or damaged samples. Moreover, the mitochondrial genome accumulates mutations at a rate that allows closely related species to be distinguished while remaining conserved enough that universal primers can bind across a wide range of vertebrate groups. By combining four independent markers in a single multiplex reaction, the new system builds redundancy into the analysis: if one marker fails to amplify or gives an ambiguous result, the other three can still deliver a species call.

The technical architecture of the assay follows the logic of targeted amplicon sequencing. Rather than sequencing entire mitochondrial genomes, which would be wasteful and impractical for degraded templates, the system uses carefully designed primer pairs to amplify short, informative regions of the four marker genes. These amplicons are then indexed with sample-specific barcodes, pooled, and sequenced in parallel on a next-generation sequencing platform. The resulting reads are processed through a bioinformatic pipeline that filters out sequencing errors and chimeric artifacts, clusters the sequences, and matches them against reference databases. This multiplex design means dozens of samples can be analyzed simultaneously, dramatically reducing both cost and turnaround time compared with running each marker separately.

What distinguishes this study from many previous metabarcoding efforts is the systematic forensic validation that accompanied the development. Following the recommendations of the International Society for Forensic Genetics (ISFG) for non-human DNA analysis, the team subjected the assay to a battery of performance tests covering the scenarios that matter most in real casework. Sensitivity testing revealed that just 10 picograms of genomic DNA from a single species—roughly the amount of DNA in a fraction of a single cell—was sufficient to detect at least one of the four markers for all species tested. When the input was raised to 100 picograms, reliable species identification was achieved using all four markers simultaneously. These thresholds place the assay firmly in the range needed for trace evidence analysis, where investigators often work with material scraped from a single bone fragment or a smudge on a knife blade.

Mixture analysis, a critical capability for food fraud detection and wildlife trafficking cases where products may contain multiple species, produced equally impressive results. In an equimolar mixture containing ten different species with a total DNA input of just one nanogram, the assay correctly identified all ten contributors. More striking still, the system detected minor components in binary mixtures down to a 99:1 ratio, meaning a species making up only one percent of the DNA in a sample could still be flagged. This level of sensitivity for minority contributors is exactly what is needed to catch adulteration, where expensive meat or seafood is diluted with cheaper substitutes at low percentages precisely to evade detection.

The degradation studies may be the most consequential for practical applications. The researchers deliberately fragmented DNA in experimental samples and then challenged the assay with the damaged templates, alongside DNA extracted from highly processed food matrices such as cooked and commercially prepared meat products. In both scenarios, the four-marker system recovered enough sequence information to make species assignments, demonstrating that the short amplicon strategy performs as intended under the harshest conditions forensic analysts are likely to encounter. Processed foods represent one of the most common contexts for species fraud, and the ability to identify constituents in cooked, canned, or otherwise transformed products closes a significant gap in food authentication testing.

Validation extended beyond the laboratory to genuine casework samples, where the tNGS-based multiplex assay demonstrated broad-spectrum vertebrate identification across real-world evidence. The authors report that these case studies confirmed the practical value of the system for three major application areas: curbing wildlife trafficking, mitigating food fraud, and facilitating biodiversity monitoring. In wildlife trafficking investigations, the ability to identify species from seized products—whether carved ivory, dried meat, traditional medicine ingredients, or leather goods—provides prosecutors with the species-level evidence needed to establish that a crime against protected fauna occurred. For food regulators, the assay offers a screening tool capable of auditing supply chains for substitution and mislabeling. For ecologists, the same chemistry can be applied to environmental DNA samples to survey vertebrate diversity in a given habitat without needing to observe or capture animals directly.

The development team, which included collaborators from the Guangzhou Public Security Bureau, the Nanchang Police Dog Base of the Ministry of Public Security, Jinan University, and the Anti-Drug Technology Center of Guangdong Province, emphasized adherence to ethical research standards throughout the study. Animal specimens were provided by the Guangzhou Zoo and the Guangzhou Wildlife Research Center with approval from the Animal Ethics Committee of those institutions. The work was funded in part by the National Natural Science Foundation of China and the Jiangxi Provincial Key Research and Development Program, reflecting the strategic priority that Chinese research agencies have placed on forensic multi-omics and wildlife protection technology.

Looking ahead, the convergence of targeted sequencing, multiplex mitochondrial barcoding, and rigorous forensic validation points toward a future where species identification becomes as routine and standardized as human DNA profiling is today. The reference sequences used in the assay are publicly accessible through the National Center for Biotechnology Information database, and the authors have made raw data available with the publication, supporting transparency and reproducibility. As sequencing costs continue to fall and reference databases expand, systems like this one could be deployed in customs laboratories, food inspection agencies, and conservation field stations worldwide. For investigators racing to document the scale of illegal wildlife trade—a market estimated to be worth billions of dollars annually—and for consumers who deserve to know what is actually in their food, a tool that can name a species from a fragment of damaged DNA may prove to be one of the most consequential forensic innovations of the decade.

Subject of Research: A mitochondrial DNA metabarcoding system based on targeted next-generation sequencing for forensic identification of vertebrate species in degraded and mixed DNA samples

Article Title: A mitochondrial DNA metabarcoding system based on tNGS enables multiplex identification of vertebrate species in samples containing degraded and mixed DNA

Article References: Liu, X., Su, C., Wei, R., Chen, X., Le, J., Xiao, G., Chang, J., Liang, S., Wu, X., Liu, C., Liu, H., Du, W., Liu, C., & Chen, L. (2026). A mitochondrial DNA metabarcoding system based on tNGS enables multiplex identification of vertebrate species in samples containing degraded and mixed DNA. International Journal of Legal Medicine. https://doi.org/10.1007/s00414-026-04024-4

Image Credits: AI Generated

DOI: 10.1007/s00414-026-04024-4

Keywords: DNA metabarcoding, targeted next-generation sequencing, mitochondrial DNA, forensic science, wildlife trafficking, food fraud, species identification, degraded DNA, cytochrome b, COI, biodiversity monitoring, vertebrate species

The Burrowing Parrot, Cyanoliseus patagonus, is no ordinary bird. It breeds in colonies dug into soft sandstone and limestone cliffs known as barrancas, and the colony near El Cóndor, beside the Río Negro estuary, is the largest known colony of any parrot species on Earth. Stretching 18.1 kilometers along the coast, it holds roughly 71 percent of the global breeding population, with long-term monitoring between 1998 and 2019 recording between 22,000 and 41,000 active nests. Understanding what these birds eat is therefore not a niche question of natural history; it is central to the survival of the majority of the species.

Historically, Burrowing Parrots were thought to feed mainly on the native vegetation of the Monte and Espinal ecoregions: seeds and fruits of chañar, caldén, algarrobo trees, berries of native shrubs such as Lycium, Discaria and Schinus, and grasses of the arid scrubland. Early naturalists, including W. H. Hudson in 1923 and Alexander Wetmore in 1926, described a diet rooted firmly in Patagonia’s native flora. The new study, published in The Science of Nature, tells a very different story. Of 202 valid plant molecular operational taxonomic units, or MOTUs, identified in the parrots’ droppings over the annual cycle, only 13 percent corresponded to native plants. Fully 40 percent were introduced species, with a further 4.5 percent presumed introduced, 12 percent ornamental garden plants, and 6.9 percent cultivated crops and pastures.

The methodology behind these numbers is a textbook example of modern molecular scatology. Between January and December 2021, the researchers collected 220 fresh fecal samples from the roosting flocks — 20 per month, except February, when the parrots mysteriously abandon the village roost. DNA was extracted from 178 samples using a stool kit optimized with bead-beating homogenization and extended incubation. Two primer sets were then amplified: one targeting the second internal transcribed spacer (ITS2) of plant nuclear ribosomal DNA, and a second targeting Bilateralia, the group that includes all animals with bilateral symmetry, to detect parasites and other animal DNA. The libraries were sequenced on an Illumina MiSeq with 250-base-pair paired-end reads.

The bioinformatic pipeline was equally rigorous. Reads were quality-trimmed with TRIMMOMATIC, merged with FLASH, de-replicated and screened for chimeras with USEARCH, and clustered into MOTUs. Each MOTU was then matched against the NCBI GenBank nucleotide database using BLASTn, with stringent thresholds: sequences had to be at least 190 base pairs long, with matches above 98 percent identity and an e-value below 0.00001. Species-level assignments required matches above 99.5 percent with consistent quality metrics across all retained hits. Negative extraction controls and PCR-grade water controls showed no contamination, and a dedicated gap analysis confirmed that the reference libraries were adequate: 69 percent of native plant species in the region have reference sequences in GenBank, rising to 97 percent at the genus level — sufficient given that 85 percent of the recovered MOTUs could be assigned to genus or better.

The seasonal patterns that emerged were striking. The parrots consumed 77 plant taxa during the breeding season, 172 during the post-breeding period, 72 in winter and 70 during pre-breeding — a statistically significant difference, with dietary diversity peaking just after the chicks fledge. This post-breeding explosion in dietary breadth coincides with the period when most plants in the region produce fruits and release seeds, and it is a critical window for juvenile survival, as young parrots must build up reserves before the harsh Patagonian winter. Non-metric multidimensional scaling and permutational multivariate analysis of variance revealed considerable overlap in diet across breeding, post-breeding and pre-breeding stages, but far less overlap with winter, when the birds turn to plants such as white spruce, velvet grass, perennial ryegrass and other introduced and ornamental species that are absent from the diet at other times of year.

Could the dominance of introduced plants be an artifact of sampling location? The researchers considered this carefully. Because samples were collected in the evening at the village roost, the diet might theoretically be biased toward items eaten near El Cóndor, where the landscape is most heavily modified. But several lines of evidence argue against it. Observations over five breeding seasons show the parrots flying over fields near the village without stopping to feed, and previous tracking studies show they forage between 58 kilometers northwest and 66 kilometers northeast of the colony. Moreover, digestive transit studies in parrots — corn-fed budgerigars empty their entire digestive tract within 26 hours — indicate that the DNA detected in evening droppings most likely reflects a full day of foraging, not just the last hours.

The most plausible explanation, the authors argue, is environmental degradation. Since the 1970s, a combination of increased rainfall and aggressive land clearing has transformed the region. In the Patagones department, natural vegetation that covered 65 percent of the land in 1975 has been reduced to an estimated 20 to 29 percent; in just three years, from 2015 to 2018, more than 216,000 hectares were cleared. In Adolfo Alsina department, home to El Cóndor, nearly 49,000 hectares were cleared between 1986 and 2006. Such landscape-scale disturbance disrupts native plant communities and opens the door to alien species. The parrots, it appears, are switching from a diet historically based on Monte and Espinal plants to one now dominated by introduced species — either a remarkable display of behavioral flexibility, or a warning sign of a suboptimal strategy that could undermine the persistence of the world’s largest parrot colony. A persistent La Niña event before and during the study may also have reduced the availability of native plants, though the authors caution that a single year of sampling cannot establish causation, and multi-year research is essential, especially as La Niña events are expected to become more frequent under climate change.

The study also delivered an unexpected bonus: a parasitological survey conducted entirely from droppings. Using the Bilateralia primer, the team identified 31 animal MOTUs, including four parasite families never before recorded in the digestive tracts of Burrowing Parrots: Gongylonematidae, which infects the oral cavity of birds and can cause starvation and death; Hymenolepididae and Onchobothriidae, both tapeworm groups previously unknown in parrots — Onchobothriidae had never been reported in any bird; and Capillariidae, thin nematodes known from captive parrots. The Gongylonematidae finding is particularly intriguing. During the 2020–2021 breeding season, at least 1,050 adult parrots died at El Cóndor — compared with the 20 to 30 typically found dead each year — and veterinary experts suspected infection rather than starvation as the primary cause. The authors stress that they can only speculate about a connection, but the possibility of a widespread Gongylonematidae infection driving that mortality event now demands investigation.

For decades, Burrowing Parrots were persecuted as agricultural pests, blamed for damage to maize, sunflowers, wheat and fruit orchards. The evidence tells a more nuanced story: systematic evaluations found that the birds affected only 0.1 to 0.4 percent of the sunflower harvest, leaving wheat and maize undamaged, and the species has been removed from Argentina’s pest-control lists. The new data reinforce this picture — cultivated plants made up just 6.9 percent of the diet, and official agricultural statistics suggest these mostly correspond to forage pastures of oats and barley rather than standing crops. As the clearance of the Monte continues and the El Cóndor colony concentrates the vast majority of the world’s Burrowing Parrots, the authors call for close monitoring of both population size and diet. The droppings collected under those Patagonian power lines have done more than reveal a menu; they have documented a dietary revolution in real time, flagged nine plant species newly introduced to the region, and possibly left a molecular clue to a mass mortality that still awaits explanation.

Subject of Research: Seasonal diet composition of Burrowing Parrots revealed by DNA metabarcoding of fecal samples

Article Title: Using next-generation sequencing to unravel the diet composition of Burrowing Parrots over the annual cycle

Article References: Masello, J. F., Failla, M., Leder, C. V., & Quillfeldt, P. (2026). Using next-generation sequencing to unravel the diet composition of Burrowing Parrots over the annual cycle. The Science of Nature, 113(5), Article 119. https://doi.org/10.1007/s00114-026-02159-3

Image Credits: AI Generated

DOI: 10.1007/s00114-026-02159-3

Keywords: Burrowing Parrot, DNA metabarcoding, next-generation sequencing, diet composition, Patagonia, El Cóndor colony, molecular scatology, introduced plants, environmental degradation, parasites, Psittaciformes, La Niña

The research team, led by Hee Jin Chung of the Mammalian Ecology and Conservation Unit at UC Davis’s Veterinary Genetics Laboratory, recruited owners of indoor–outdoor cats in Davis and Sacramento, California. Participants were given simple kits containing ethanol-filled tubes, nitrile gloves, and a printed log, and were asked to collect five of their cat’s fecal samples over several weeks, along with a sample of whatever food the cat was being fed. Between November 8 and December 21, 2023, the team received 38 scats from eight neutered house cats—three males and five females—whose samples were, for anonymity, labeled Cat A through Cat H. Most samples came straight from litter boxes and were collected within hours of defecation, making them unusually fresh for molecular work.

The technical core of the study was DNA metabarcoding, a sequencing approach that identifies the mixture of DNA left behind in feces. The researchers amplified two mitochondrial markers: the 12S rRNA gene to detect vertebrate prey and the 16S rRNA gene to detect invertebrates. Because cat DNA overwhelmingly dominates cat feces, the team designed a custom blocking oligonucleotide—a short synthetic molecule carrying a three-carbon spacer—that binds to domestic cat sequences and stalls their amplification, allowing dietary DNA to be recovered more easily. Sequencing was performed on an Illumina platform, and the resulting reads were processed with cutadapt and DADA2, which identify distinct amplicon sequence variants, before taxa were assigned using BLAST searches against custom and NCBI reference libraries. Samples below strict read-count and identity thresholds were discarded to guard against contamination.

The results were striking, and somewhat humbling for anyone who assumes their cat is quietly devastating the neighborhood. Of 32 analyzable scat samples, roughly a third contained no vertebrate DNA at all except that of the cat itself. Most of the remainder revealed only anthropogenic food items—chicken, pig, turkey, and fish from the drum, hake, and herring families—matching the provisioned pet foods owners submitted for comparison. In total, only a single scat, produced by Cat H, contained wild vertebrate prey: the California vole, Microtus californicus, a common rodent in the region. The cat that produced it had not been seen with any prey by its owner in the preceding 24 hours.

Even more revealing were the three cases where owners did witness their cats carrying prey—a live house mouse caught indoors, a small unidentified rodent brought to the door, and a lizard caught in front of the home. In every instance the prey was alive and intact, and in every instance the corresponding scat, produced within 24 hours, contained no wild prey DNA whatsoever. The findings suggest that domestic cats frequently hunt without consuming what they catch, consistent with earlier camera-collar studies showing that satiated cats hunt for enrichment, practice, or caching rather than nutrition. They also imply that significant prey consumption is needed before prey DNA becomes detectable in feces, meaning molecular scat analysis and owner reports capture different facets of the same hunting behavior—and should be used together.

The comparison between provisioned food and scat also yielded a methodological surprise. Chicken and pig DNA appeared in all four collected food samples, as expected, but recovery of those ingredients in the corresponding scats varied widely. Chicken, present in nearly every relevant food, showed up in 14 of 15 expected scat samples, making it the most digestible and detectable ingredient. By contrast, the two prescription diets—a hydrolyzed-protein formula and a kidney-care wet food—showed the poorest post-digestion recovery, likely because heavy industrial processing degrades DNA before the food even reaches the bowl. Notably, several scats from cats eating animal-based diets contained no animal DNA other than cat DNA, a finding with implications beyond cats: urban wildlife studies routinely identify pet food as an anthropogenic food source in carnivore scats, and this study suggests such DNA may often be too degraded to detect.

The team also tested a cost-saving shortcut that could matter for future studies: pooling. Because DNA extraction and sequencing are expensive, they homogenized subsamples of three to five scats from each cat into a single pooled sample, then compared pooled results against individually extracted samples. The answer was mixed. Common items such as chicken were recovered reliably regardless of pooling, and for two cats the two approaches matched perfectly. But the study’s only wild prey detection—the California vole—appeared only in the individually extracted sample and vanished in the pooled version. When the target of a study is a rare or rarely consumed prey item, the authors conclude, pooling samples before extraction can erase exactly the signal researchers are looking for.

The invertebrate results illustrate another caution. The 16S data were compromised by heavy contamination in negative controls and poor amplification, and although Orthoptera, flies, true bugs, jumping spiders, and noctuid moths were detected in some scats, the team excluded the invertebrate dataset from formal analysis. Primer bias is a further limitation: the 12S primers used here perform poorly on reptiles and amphibians, so the absence of lizard DNA in the scats—despite one owner reporting a caught lizard—may reflect molecular bias rather than true absence. The authors recommend that future studies pair molecular methods with morphological analysis of scat contents to avoid missing entire taxonomic groups.

Despite its small sample size and short duration—cats were sampled for an average of about 12 days—the study demonstrates that owned cats, paired with their willing owners, can serve as a viable study system for predator diet research. Citizen-science sample collection slashes the cost and effort of fieldwork, while owner logs add behavioral context that scat alone cannot provide. And because neither sterilization nor regular feeding reliably suppresses hunting, even well-fed, neutered cats remain relevant to wildlife conservation, particularly where vulnerable prey such as the endangered Amargosa vole, a California vole subspecies, persist. The broader lesson is that a single tool will never fully capture the ecology of a predator that hunts both out of hunger and out of instinct. DNA metabarcoding catches the meals owners never see; owner questionnaires catch the trophies cats bring home uneaten. Used together, they offer the clearest picture yet of what the world’s most popular pet is really doing to the wildlife in its own backyard.

Subject of Research: DNA metabarcoding of owner-collected scat samples to assess the diet and wild prey consumption of owned domestic cats.

Article Title: Using DNA Metabarcoding and Citizen Science to Assess the Diet of Owned Domestic Cats

Article References: Chung, H. J., Vanderzwan, S. L., & Sacks, B. N. (2026). Using DNA Metabarcoding and Citizen Science to Assess the Diet of Owned Domestic Cats. Ecology and Evolution, 16(9), Article e74404. https://doi.org/10.1002/ece3.74404

Image Credits: AI Generated

DOI: 10.1002/ece3.74404

Keywords: domestic cat, DNA metabarcoding, citizen science, diet analysis, wildlife conservation, California vole, pet food, hunting behavior, scat samples, owned cats, Metabarcoding, Citizen