The study was conducted from 2022 to 2024 at the Polli Horticultural Research Centre in southern Estonia. The adjacent orchards shared the same Albic Luvisol soil type, MM106 rootstock, standard-spindle training system, planting density and ground-cover management, and were separated by about 300 metres. The organic orchard had been managed under its system since 2008 and the IPM orchard since 2010, giving the sites 14 and 12 years of management history when observations began. The study examined the Estonian cultivars “Katre” and “Krista” and the Belarusian cultivar “Alesja,” assessing yield, fruit chemistry, peel colour, firmness, soil chemistry, earthworms and springtails. These were orchard-level observations from two specific sites rather than a randomized comparison of many independent orchards.

The orchards differed chiefly in crop protection and fertilisation. Neither used herbicides. The IPM orchard received registered synthetic insecticides, including deltamethrin and flonicamid, and fungicides including cyprodinil, difenoconazole and dithianon. The organic orchard relied on products permitted in organic production, including azadirachtin and Bacillus thuringiensis, and no fungicides were applied there. In the fertilised years, nitrogen inputs were substantially higher in the IPM orchard: a compound fertiliser in 2022 supplied 36.4 kg N per hectare, while ammonium nitrate in 2024 supplied 41.4 kg N per hectare. The organic orchard received poultry manure-based fertiliser supplying 11.8 kg N per hectare per application. No fertiliser was applied in either orchard in 2023. Because management history, crop protection and fertiliser inputs were not independently manipulated, their separate effects could not be determined.

Yield was evaluated in 2022, the only year for which a representative crop could be compared. Severe frosts in early May 2023 destroyed the crop, and frost during flowering in 2024 produced non-representative crop loads, so yield was not assessed in those years. Total yield was significantly higher under IPM management for “Katre” and “Alesja,” while no significant system difference occurred for “Krista.” Averaged across cultivars, total yield was 42.1 ± 9.1 kg per tree in the IPM orchard and 32.1 ± 18.4 kg per tree in the organic orchard. Fresh-market yield was also higher overall under IPM, at 28.1 ± 7.2 versus 19.7 ± 12.6 kg per tree, but the proportion classified as fresh-market fruit did not differ consistently between systems. The higher fresh-market output therefore reflected greater total production rather than a universal improvement in marketability. “Alesja” was an exception: only 49.3% of organically grown fruit met fresh-market standards, compared with 72.8% under IPM, largely because of greater codling moth damage in the organic orchard.

Because fertilisation was not experimentally separated from the production systems, the study could not determine whether nutrient supply or another aspect of management caused the observed differences. The IPM orchard nevertheless produced fruit with higher average nitrogen concentrations in 2024, while organic apples had higher average phosphorus and potassium. Fruit firmness ranged from 52 to 82 N in 2022 and 40 to 58 N in 2024, but did not differ significantly between cultivation systems for any cultivar in either year. Colour, measured only in 2024, showed a clearer system-level pattern. Averaged across cultivars, organic apples had lower lightness, higher redness and chroma, and lower hue angle, indicating darker, redder and more intensely coloured peel. Cultivar-specific differences were less consistent, with organic “Alesja” showing significantly greater chroma than its IPM counterpart while several other within-cultivar comparisons were not significant. The study associated these patterns with the different nutrient regimes, but it did not establish nitrogen availability as the cause.

Taste-related measures followed no single management pattern. Soluble solids content was lower in IPM-grown “Katre” and “Krista” in 2022, but the reverse occurred for “Alesja”; in 2024, soluble solids were again lower in IPM “Katre” while “Alesja” was lower. Titratable acidity was higher in organic “Katre” and “Alesja” in both sampled years, but the overall ratio of soluble solids to titratable acids was higher under IPM when averaged across cultivars. Some contrasts reached levels that consumers could potentially perceive: the study cited thresholds of more than 1 °Brix for soluble solids and more than 0.08% for titratable acidity. These included 1.1 °Brix for “Krista” in 2022 and acidity differences of 0.10–0.17% for “Katre.” Individual sugars did not show a consistent system effect, and the authors noted that genotype and weather appeared to influence fruit composition more strongly than management history.

Antioxidant measurements produced a similar cultivar-dependent pattern. Organic “Katre” had significantly higher total polyphenol content in both 2022 and 2024, but the same difference was not detected for “Krista” or “Alesja.” “Alesja” had the highest total polyphenol and anthocyanin concentrations regardless of cultivation system, supporting the importance of genotype. Anthocyanins averaged higher in organic fruit in 2022, but the management effect disappeared in 2024, and there was no significant overall difference in ascorbic acid content. The contrast between years coincided with contrasting weather: a cool spring and dry June preceded a warm August in 2022, whereas 2024 brought exceptionally dry May conditions followed by above-average temperatures and wetter late-season conditions. The researchers said these climatic differences could alter pigment and vitamin C accumulation, making it inappropriate to treat the two years as equivalent tests of a stable management effect.

Soil chemistry showed significant differences between the orchards. Organic orchard soil had higher pH, phosphorus and calcium in each sampling year. Its pH in KCl ranged from 5.84 to 6.27, compared with 4.94 to 5.24 in the IPM orchard. Total phosphorus was 109–122 mg per kilogram in the organic soil and 47–55 mg per kilogram in the IPM soil, while calcium ranged from 969 to 1,050 versus 658 to 726 mg per kilogram. Magnesium, total nitrogen and total potassium did not differ significantly. The different fertiliser sources were plausibly involved: the organic orchard’s poultry manure product supplied calcium and organic matter, but fertiliser type could not be isolated from the orchards’ longer management histories or site-specific conditions.

Earthworm results showed contrasting patterns between total abundance and community composition. Six species were recorded in both systems, but total abundance was significantly higher in the IPM orchard in 2024, with mean abundance across the three years reported as 148.0 ± 28.5 individuals per square metre, compared with 96.4 ± 9.1 in the organic orchard. The pattern was not explained by permanent dominance of one ecological group. Instead, the organic orchard consistently had a higher share of anecic earthworms, which occupy deep permanent burrows and feed at the surface, including A. longa. Exploratory ordination associated organic samples with higher pH, phosphorus, calcium, magnesium and microbial-activity indices, while IPM samples were positioned closer to precipitation, moisture and temperature variables. These were visual associations rather than formal causal tests: the analysis used only six orchard-year combinations, and soil microbial respiration and biomass lacked independent within-orchard replication.

Springtails did not show a significant overall abundance response to management. Across the study, total abundance was not significantly affected by year, cultivation system or their interaction, although the organic orchard numerically exceeded IPM in 2022 and 2023 before the order reversed in 2024. Ecological life form did matter: euedaphic springtails living within the soil matrix were significantly more abundant than hemiedaphic forms. The organic orchard generally recorded more species, including 20, 22 and 21 in the three years, compared with 18, 23 and 17 under IPM, while the IPM orchard had a higher share of euedaphic forms in two years. Exploratory correlations linked community differences to soil moisture, precipitation, nitrogen, pH and phosphorus rather than demonstrating a direct effect of cultivation system.

Together, the results offer a nuanced picture of long-term apple production under Nordic and Baltic conditions. IPM management was associated with greater productivity for two cultivars, and organic management with more intense peel colour, higher soil pH, more phosphorus and calcium, and a larger proportion of anecic earthworms. Neither system consistently produced sweeter, more acidic or more antioxidant-rich fruit across cultivars and years. The study’s strongest limitation is also its most important caution: each system was represented by only one orchard, so cultivation method was confounded with orchard identity, microclimate and management history. Trees and soil sampling points were subsamples rather than independent orchard-level replicates. Replicated comparisons across multiple orchards would be needed before these site-specific patterns could be generalized to organic and IPM production systems.

Subject of Research: Comparison of apple quality and soil biological diversity in long-term organic and integrated pest management orchards

Article Title: Apple quality and soil biological diversity in long-term organic and IPM apple orchards

Article References: Moor, U., Kuu, A., Kahu, K., Põldma, P., & Rätsep, R. (2026). Apple quality and soil biological diversity in long-term organic and IPM apple orchards. Frontiers in Sustainable Food Systems, 10, Article 1943487. https://doi.org/10.3389/fsufs.2026.1943487

Image Credits: AI Generated

DOI: 10.3389/fsufs.2026.1943487

Keywords: apple orchards, organic farming, integrated pest management, soil biodiversity, earthworms, springtails, fruit quality, peel colour, antioxidants, Estonia, Apple, quality

The study was conducted in the limestone quarry near the village of Saskhori, southeast of Kaspi in Georgia’s Kartli Region. The quarry is owned by the Heidelberg Cement Company, and mining began in 2018. A survey conducted in 2018 before mining activities started had recorded 51 oribatid mite species across the area. The 2022 investigation repeated sampling across the quarry and adjacent landscapes to examine community composition, diversity, abundance and possible changes associated with anthropogenic disturbance.

Researchers collected soil in February, April and July 2022 from seven locations. The habitats included degraded steppe with rural and invasive plants, Mediterranean-type deciduous drought-resistant shrubbery, bare limestone bedrock, degraded xero-thermophilous oak forest, shrubland, an almond garden and mixed oak-hornbeam woodland and shrubbery. At each site, three 10-cubic-centimetre soil samples were randomly collected with a steel corer. In total, 63 samples were extracted for seven days in Berlese-Tullgren apparatuses, and the recovered material was preserved in 96% alcohol.

Specimens were mounted on temporary slides with lactic acid and identified microscopically. The analysis used taxonomic identification keys, rarefaction and extrapolation with 100 bootstrap replicates, and comparisons of species richness, individual density, Shannon diversity, Pielou evenness and Sørensen similarity. Neighbour-joining clustering based on Euclidean distance was also applied. The deposited specimens were assigned to the collection of the Institute of Zoology at Ilia State University in Tbilisi.

The survey yielded 983 mites representing 52 species, 41 genera and 28 families. Site Sa2, in Mediterranean-type deciduous drought-resistant shrubbery, had the highest richness, with 27 species, while Sa1, Sa4 and Sa7 each contained 22. Across habitat types, shrubbery was richest with 37 species, followed by the xero-thermophilous oak forest and mixed oak-hornbeam vegetation with 32. The almond garden’s rural and urban habitat contained 10 species, the lowest total recorded. Sa2 also had the largest number of individuals, with 191, followed by Sa1 with 185 and Sa3 with 175.

Xenillus tegeocranus was the most abundant species, with 120 specimens from six sites. Aleurodamaeus setosus had 106 specimens, Punctoribates punctum 85 and Ceratoppia bipilis 66, also across six of the seven sites. Seventeen species occurred at only one location. Shannon diversity was highest at Sa2, where H equalled 2.72, and lowest at Sa6, where H was 1.97 in Table 3. Pielou evenness ranged from 0.77 at Sa1 to 0.87 at Sa5 and Sa6. Sørensen-based clustering placed Sa1 with Sa2 and Sa3 with Sa4, while the Sa6 community was the most distinct from those in natural and semi-natural habitats.

Rarefaction and extrapolation indicated that additional sampling was likely to detect more species. The model estimated a maximum expected richness of 67 species, with an upper confidence limit of 88. Only 29 species, or 39% of the taxa reported in the two surveys, were shared between the 2018 and 2022 studies. The authors said the large difference in composition was probably driven more by incomplete sampling in both investigations than by faunal turnover over such a short interval. They also observed changes in relative abundance: several species found at one location in 2018 occurred at multiple sites in 2022, and Aleurodamaeus setosus and Punctoribates punctum joined Xenillus tegeocranus and Scheloribates laevigatus as broadly distributed species.

One taxonomic finding was the first Caucasus record of Liacarus oribatelloides, a species described in 1956 from the Czech Republic. Before the Saskhori finding, it had been reported from several Central European locations, including southern Germany, Austria, Italy, Slovakia, Poland, the Central Alps and the Tatra Mountains. The Saskhori specimens measured 1084–1198 micrometres in body length and 657–728 micrometres in width. They were distinguished from L. coracinus by their elongated, dark-brown to black body, strongly elongated lamellar cusp tips, a longer leg IV and a distinct inner tooth on the femur of leg IV.

The taxonomic status of L. oribatelloides remains uncertain. The latest world catalogue cited by the study treats it as a senior synonym of L. coracinus, while other publications have treated it as valid. The authors therefore stated that molecular genetic analysis is needed to clarify its status and interspecific boundaries within Liacarus. At the community level, the survey found lower mite density and diversity at heavily grazed sites where soil structure was destroyed, while more natural vegetation supported richer communities. The authors associated the observed community change most probably with ongoing limestone mining, but emphasized that the study’s extent and design do not permit predictions about future faunal changes.

Subject of Research: A 2022 field survey of oribatid mite species diversity, abundance and taxonomy across a Georgian limestone quarry and adjacent habitats.

Article Title: Soil mite ( Acari : Oribatida ) communities in the limestone quarry of Saskhori (Gerogia)

Article References: Arabuli, T., & Gogshelidze, M. (2023). Soil mite (Acari: Oribatida) communities in the limestone quarry of Saskhori (Gerogia). Caucasiana, 2, 189-197. https://doi.org/10.3897/caucasiana.2.e110495

Image Credits: AI Generated

DOI: 10.3897/caucasiana.2.e110495

Keywords: oribatid mites, soil biodiversity, Saskhori quarry, Georgia, habitat disturbance, limestone mining, species richness, ecological monitoring, Caucasus fauna, Liacarus oribatelloides, Soil, mite

The study, conducted from March 2021 to January 2023, examined Bani Valley in Kathua district at latitudes 32°41′23″–32°43′15″ N and longitudes 75°43′59″–75°48′11″ E. The sampled habitats included oak-dominated forest, apple orchards and crop fields where maize and mustard were cultivated in rotation. Earthworm sampling followed the Tropical Soil Biology and Fertility method at bimonthly intervals. During each sampling, researchers selected three 100 m² plots in each habitat and extracted five monoliths measuring 25 cm by 25 cm and 30 cm deep, without resampling the same area.

Adult earthworms were extracted, counted and weighed to determine fresh biomass, while representative specimens were preserved for taxonomic identification. Identification followed standard earthworm monographs. The researchers also measured soil temperature, moisture, pH, electrical conductivity, texture, organic carbon, nitrogen, phosphorus and potassium. A phylogenetic analysis used partial mitochondrial cytochrome c oxidase subunit I sequences, alignment in MEGA X, and a Maximum Likelihood reconstruction with the Tamura–Nei model and 1,000 bootstrap replicates.

Lumbricidae dominated the eight-species community, with Aporrectodea caliginosa caliginosa, Aporrectodea caliginosa trapezoides, Octolasion tyrtaeum, Dendrodrilus rubidus and Bimastos parvus. Moniligastridae was represented by Drawida japonica and Drawida nepalensis, and Megascolecidae by Amynthas corticis. Six species were categorized as endogeic, while Bimastos parvus was epigeic and Amynthas corticis was epi-endogeic. Octolasion tyrtaeum had the highest mean density in both study years: 34.31 ± 2.54 individuals per m² in 2021–22 and 27.91 ± 1.88 in 2022–23. It also had the highest mean biomass, at 16.47 ± 1.22 g/m² and 13.40 ± 0.90 g/m², respectively.

Seasonality was pronounced. The monsoon period from July to September was the most favorable overall, and density, biomass and species richness reached their highest values in July of both years. In July 2021, crop-field density reached 188.80 individuals per m², compared with 137.60 in the orchard and 96.00 in the forest. The minimum values were not uniform across all measures: forest density was lowest in March of both years and January 2023, forest biomass was lowest in January 2023, orchard density and biomass were lowest in January 2023, crop-field density was lowest in January 2022 and January 2023, and crop-field biomass was lowest in May 2022. The first study year recorded significantly higher density and biomass than the second.

Diversity indices varied significantly among habitats and months for dominance, Simpson’s index and the Shannon–Wiener index, while differences in evenness were not significant. Shannon–Wiener values ranged from 0.50 to 1.67 in forest, 0.64 to 1.97 in orchards and 0.80 to 1.92 in crop fields. The study reported significant differences between forest and both other habitats, but no significant difference between orchards and crop fields. The maximum Shannon–Wiener value in each habitat occurred in July 2022, while the minimum occurred in January 2023.

The Maximum Likelihood reconstruction identified three main clades and was largely consistent with classification at genus level. Drawida nepalensis and Octolasion tyrtaeum nevertheless clustered despite belonging to different families. The authors stated that this intergeneric grouping could reflect convergent mitochondrial evolution or unresolved divergence caused by limited variation in COX1, and that it warrants further investigation. The analysis therefore provided a baseline for relationships among the eight species rather than resolving their evolutionary placement conclusively.

Canonical correspondence analysis indicated associations between species distributions and measured soil properties. For density, the first canonical axis explained 53.47% of the total variance and was associated with temperature, moisture and pH; the second explained 21.57% and was associated primarily with organic carbon and nitrogen. For biomass, the first two axes together explained 77.85% of the variance. Bimastos parvus, Dendrodrilus rubidus, Drawida nepalensis, Drawida japonica and Amynthas corticis were associated with different combinations of temperature, moisture, pH and electrical conductivity. Aporrectorea caliginosa caliginosa and A. caliginosa trapezoides aligned with phosphorus, organic carbon and nitrogen. Octolasion tyrtaeum was associated with different ecological conditions, consistent with its abundance throughout the year. These ordination results describe statistical associations and do not establish that particular soil properties caused the observed distributions.

All eight species were reported as new records for Kathua district, bringing its documented earthworm diversity to 18 species. Dendrodrilus rubidus was not found in comparisons with adjacent parts of the western Himalayan Region and was reported for the first time from Bani Valley, although the authors noted that further investigation was needed. The study was limited to one valley, three selected habitat types and two years of sampling, so it provides a localized baseline rather than a comprehensive picture of Himalayan earthworm diversity.

Subject of Research: Earthworm diversity and habitat-related distribution patterns in Bani Valley

Article Title: Earthworm diversity in an unexplored Himalayan landscape: Patterns across forest, orchard and crop field ecosystems

Article References: Lal, M., Bhagat, A., Ahmed, S., & Kaur, A. (2025). Earthworm diversity in an unexplored Himalayan landscape: Patterns across forest, orchard and crop field ecosystems. One Ecosystem, 10, Article e166980. https://doi.org/10.3897/oneeco.10.e166980

Image Credits: AI Generated

DOI: 10.3897/oneeco.10.e166980

Keywords: earthworms, Bani Valley, Himalayas, soil biodiversity, earthworm species, habitat comparison, soil properties, phylogenetics, Jammu and Kashmir, Earthworm, diversity, unexplored

The study examined Armadillidium nasatum , A. vulgare , Haplophthalmus danicus , Porcellio dilatatus , P. laevis , P. scaber and Porcellionides pruinosus , seven terrestrial isopods treated as exotic in Japan and associated originally with Europe or the Mediterranean region. The underlying Japanese database contained 17,412 specimens compiled from 159 publications, museum records and the first author’s personal collection. After duplicate locations were excluded, the seven species were represented by 1,516 Japanese sites, while the European and North American occurrence datasets supplied 4,135 and 1,953 locations, respectively.

Five species were first reported in Japan in 1927; A. nasatum and P. dilatatus were first reported in 1943. Researchers used Maxent version 3.4.1 to construct environmental niche models from 19 bioclimatic variables in WorldClim version 2.0, mapped at five-arc-minute resolution. The variables included measures of temperature and precipitation.

To reduce multicollinearity, highly correlated predictors were removed when the absolute value of their Pearson correlation coefficient was at least 0.75. Models used linear and quadratic features to describe relationships between occurrence probability and environmental conditions while limiting overfitting. Because the records came from non-random sources, the researchers generated a kernel-density estimate of sampling bias and selected 10,000 background points weighted by that surface, creating a target-group background intended to account for uneven collection effort.

Two modelling approaches were compared for each species. Regional models used occurrence records from Japan alone, whereas global models combined Japanese records with those from Europe and North America. Training area under the curve, or AUC, ranged from 0.681 to 0.910 for the global models and from 0.712 to 0.857 for the regional models.

AUC values above 0.9 indicate high discriminatory performance, values from 0.7 to 0.9 represent reasonable or moderate performance, and values from 0.5 to 0.7 indicate poor performance. Global models performed better for A. nasatum , A. vulgare and P. dilatatus . The researchers used the global approach to map potential Japanese distributions because records confined to an invaded country may understate the full environmental range occupied by a species in its native and other invaded regions.

Temperature-related variables supplied most of the strongest climatic signals in the global models. Annual mean temperature contributed more than 25 percent for three species: A. nasatum , H. danicus and P. scaber . Mean diurnal temperature range exceeded a 25 percent contribution for five species: A. vulgare , H. danicus , P. laevis , P. scaber and P. pruinosus .

Temperature seasonality was also a major predictor for P. dilatatus , contributing 37.6 percent. Among precipitation variables, seasonality contributed more than 25 percent for A. nasatum , P. dilatatus and P. laevis , while precipitation in the wettest month was especially important for A. nasatum , exceeding 65 percent contribution and permutation importance. The response curves revealed shared and species-specific temperature patterns.

Annual mean temperature responses differed among the remaining species: A. nasatum , H. danicus and P. scaber were associated with temperatures above 15°C, while P. pruinosus showed a hump-shaped response across a more moderate range of approximately 15–25°C. The study’s authors noted that the annual mean temperatures assigned probabilities above 0.5 covered roughly 10–25°C across most of Japan except mountainous areas, suggesting that annual mean temperature alone was not the principal national-scale constraint for these species. Global potential distributions generally included western Honshu, Shikoku and Kyushu, although their boundaries varied among species.

Suitable areas for A. vulgare , P. scaber and P. pruinosus extended farther inland than those for A. nasatum and H. danicus . The projected range for P. scaber also included coastal Hokkaido, while that of P. laevis was concentrated more heavily in southwestern Japan. For P. dilatatus , the global and regional models both identified most of Kyushu and Shikoku, but the regional model additionally projected suitable coastal areas of Honshu and southern Hokkaido.

The broader global projections for the other six species suggest that their Japanese occurrence records had not yet reached all areas classified as climatically suitable, not that those areas will inevitably be occupied. Invasion stages were inferred by plotting regional against global model probabilities and dividing the results at a probability of 0.5. Areas classified as highly suitable by both models represented stabilising populations.

High global probability combined with low regional probability indicated colonising populations, whereas low probability in both models identified sink populations. A high regional probability paired with low global probability was interpreted as a locally adapted population. A. vulgare , H. danicus , P. laevis , P. scaber and P. pruinosus contained mixtures of stabilising and colonising areas, with several sink areas also identified.

A. nasatum was composed mainly of stabilising areas and one sink, while P. dilatatus produced the pattern assigned to local adaptation. These labels describe relationships between model predictions rather than observed demographic outcomes. For example, a colonising classification means that an area is climatically suitable in the global model but poorly represented by the species’ Japanese regional occurrence pattern; it does not establish a population trajectory or guarantee establishment.

Likewise, a sink classification is consistent with the presence of a species in an area predicted to be unsuitable, including cooler inland and northern locations, but it does not demonstrate that a population is declining. The four categories did not form sharply separated geographic regions. The authors also warned that occurrence records could not cover every part of the species’ ranges and that the projected maps might change as a larger, more complete database became available.

A. vulgare had the widest recorded Japanese range, extending from 43°10′ north to 24°45′ north, and occurred at 770 sites. P. scaber was recorded at 393 sites and was the only species commonly reported in Hokkaido. The Japanese records for A. nasatum , P. dilatatus and P. laevis numbered 20, seven and 32 sites, respectively, while P. pruinosus occurred at 174 sites and reached Iriomotejima Island at 24°16′ north, the southernmost location in the dataset.

The authors considered the short time since the first Japanese reports of A. nasatum , together with its large projected suitable area and introduction to suitable areas, one possible reason for its limited number of records. They also suggested that the ecological niche and areas of introduction were more relevant than elapsed time to the narrow Japanese range of P. dilatatus . The results show why occurrence records from an invaded region alone may underestimate the potential range of these seven exotic isopods.

Combining Japanese, European and North American data produced wider projections for six species and exposed areas where further establishment may be possible. The analysis did not establish ecological harm, human exposure or the consequences of future expansion, and its macro-scale climate models did not include every local influence on isopods. Within those limits, the study identifies temperature and diurnal temperature variation as major climatic correlates and suggests that six of the seven modelled species retained geographic scope for potential expansion beyond their documented Japanese ranges.

Subject of Research: Ecological niche modelling of seven exotic terrestrial isopod distributions and invasion stages in Japan

Article Title: Invasion stages and potential distributions of seven exotic terrestrial isopods in Japan

Article References: Karasawa, S., & Nakata, K. (2018). Invasion stages and potential distributions of seven exotic terrestrial isopods in Japan. BioRisk, 13, 53-76. https://doi.org/10.3897/biorisk.13.23514

Image Credits: AI Generated

DOI: 10.3897/biorisk.13.23514

Keywords: terrestrial isopods, Japan, ecological niche modelling, species distribution models, invasive species, climatic niche, temperature variables, Maxent, invasion stages, soil biodiversity, Invasion, stages

Researchers from the University of Florida surveyed nematode communities in four strawberry fields in Hillsborough County, three managed conventionally and one managed organically. Sampling took place in June 2021, roughly two months after the strawberry crop was terminated, when soil temperatures were among the hottest of the year. Using a gas-powered auger, the team collected soil cores from four separate depths, from the surface down to one metre, at known hot spots of the northern root-knot nematode, Meloidogyne hapla, a pest likely introduced to Florida on infected transplants from out-of-state nurseries.

Each sample was split and processed two ways. The traditional approach involved extracting live nematodes from the soil using centrifugal flotation, counting them under an inverted microscope and identifying plant parasites to genus or species by morphology, while free-living worms were assigned only to broad trophic groups. The second approach was a targeted form of mitochondrial metagenomics, or mtMG. Whole DNA was extracted from the entire nematode suspension, sequencing libraries were prepared and then enriched for mitochondrial DNA using hybridisation capture probes designed against nematode mitochondrial genomes. The samples were sequenced on an Illumina NovaSeq 6000, and the resulting reads were assembled into contigs and matched against a curated nematode mitochondrial reference database.

The molecular workflow required careful quality control. Of 301 contigs that passed initial classification, 35 were discarded after phylogenetic tree analysis revealed poor alignments suggestive of misidentification, a problem concentrated in the suborder Tylenchina. The team also screened for haplotypes, closely related sequence variants within species, using maximum likelihood trees with bootstrap support, distinguishing genuine population diversity from assembly errors. This conservative filtering proved essential for trustworthy species-level detections.

The comparison revealed significant differences in both richness and composition between the two methods. The annotated COX1 mtMG approach, which identified mitochondrial contigs by open reading frame annotation rather than read mapping, recovered far more taxa than the read-mapping variants and came closest to mirroring the morphological data. It tentatively identified 14 bacterial-feeding species across nine genera that morphology could only label as ‘bacterial feeders’, and it detected animal-parasitic nematodes, likely present as eggs or unidentifiable juvenile stages, that microscopy missed entirely in every sample.

Yet the molecular method had its own blind spots. Morphology detected plant parasites such as the sting nematode Belonolaimus longicaudatus, Nanidorus minor and Tylenchorhynchus species that mtMG failed to recover, almost certainly because their mitochondrial reference sequences are missing from the database. Conversely, mtMG picked up Mesocriconema species and the dagger nematode Xiphinema brevicollum that microscopy had not found. The two approaches also disagreed on omnivores and predators, which appeared only in the morphological counts, probably because their low abundance meant too few sequencing reads to assemble.

Where the methods agreed, the agreement was powerful. Both consistently detected Meloidogyne across all fields, and mtMG went further, precisely identifying M. hapla in three fields while also revealing the co-occurrence of M. javanica, M. incognita and M. luci in the organic field, along with multiple haplotypes of M. hapla that morphology cannot distinguish. This capacity to resolve species and population-level variation matters enormously, because species identity can dictate which management strategy a grower should adopt, and haplotype diversity has been linked to emerging nematicide resistance.

Despite their differences in detected taxa, both methods converged on the same ecological conclusions. Field identity was the dominant factor structuring nematode community composition, reflecting each field’s distinct management history, and sampling depth played a significant role as well. The mtMG data in particular showed that Meloidogyne species were recovered throughout the entire one-metre soil column, supporting earlier evidence that plant-parasitic nematodes migrate vertically through Florida’s deep sandy soils, likely in response to heat, tillage or fumigation. This vertical movement has practical implications, since deep soil layers may act as reservoirs from which root-knot populations re-establish after fumigation.

The authors conclude that mtMG and morphology are highly complementary tools, and that combining them yields a far more accurate picture of nematode diversity than either alone. They identify four priorities for improving the molecular approach: expanding the phylogenetic coverage of the mitochondrial reference database, refining contig filtering and classification pipelines, improving detection of under-represented trophic groups such as omnivores and predators, and adding reference sequences for rare crop pests. As the database grows, mtMG should become increasingly capable of flagging subtle genetic variants, including nematicide-resistant haplotypes, giving growers an earlier warning than morphology could ever provide.

For Florida’s strawberry industry, which produced roughly 511 million dollars’ worth of fruit in 2022 across some 12,000 acres, the stakes are considerable. Sting and root-knot nematodes remain among the most damaging pests growers face, and management increasingly relies on targeted, environmentally sustainable approaches rather than broad-spectrum fumigants. Accurate, species-level monitoring of entire nematode communities, the kind of monitoring this study shows is achievable when molecular and morphological methods are deployed together, could become a cornerstone of that transition.

Subject of Research: Comparison of mitochondrial metagenomics and morphological identification for surveying nematode communities in strawberry fields

Article Title: Improving understanding of nematode communities in agricultural settings: a comparison of mitometagenomics and morphology

Article References: Gendron, E. M. S., Oliveira, C. J., Desaeger, J., & Porazinska, D. L. (2024). Improving understanding of nematode communities in agricultural settings: a comparison of mitometagenomics and morphology. Metabarcoding and Metagenomics, 8, Article e123387. https://doi.org/10.3897/mbmg.8.123387

Image Credits: AI Generated

DOI: 10.3897/mbmg.8.123387

Keywords: nematodes, mitochondrial metagenomics, morphology, strawberry, Florida, plant-parasitic nematodes, Meloidogyne, soil biodiversity, metabarcoding, agriculture, soil depth, pest management

The conversation began, fittingly, with a classification problem. Zanella was holding a zoogenic organic horizon, called zoOH, litter transformed into humus largely by arthropods, and an organo-mineral A horizon, called meA, made of stable aggregates between one and four millimeters in diameter produced by earthworms. In an orderly soil profile these horizons sit neatly one above the other, but wild boars rooting through the litter with their snouts had scrambled the sequence entirely. Zanella joked that classification systems would need new categories to handle such chaos. Pignatti smiled and offered a broader lesson: field scientists arrive with clear ideas, then the messy reality of nature blurs them. The encounter set the tone for everything that followed, an attempt to reconcile tidy scientific frameworks with an ecosystem whose boundaries refuse to stay still.

Walking through a holm oak forest dotted with circular pools of stagnant water, the two men turned to the discipline of phytosociology, the classical Braun-Blanquet tradition of mapping plant communities using characteristic species. The problem, they agreed, is that these diagnostic species by definition have narrow ecological ranges, which makes them scarce precisely along the boundary lines where cartographers need them most. Mapping plant landscapes without leaving large unclassifiable gray areas is nearly impossible. Pignatti described himself not as a phytosociologist but as an expert in vegetation ecology, and recalled that the late Lucio Susmel had written a well-documented critique of the phytosociological approach as early as 1959. Yet in the field, both men admitted, even skeptics are forced to imitate the phytosociologists, reading the colors and structure of vegetation to recognize units within a landscape.

Their shared conclusion was subtle. Plant communities may be real, evolving and shifting entities whose members, in Pignatti’s words, communicate with each other and with animals simply to survive, yet they remain poorly defined in space, existing like objects in a kind of black hole shaped by ecological attractors that themselves keep changing. This echoes Tansley’s foundational 1935 concept of the ecosystem and its crucial insistence on indivisibility: when we try to understand ecological functioning, we cannot separate living beings from each other, nor any organism from its environment. Ecosystems, the two naturalists argued, should in principle continue evolving into the future, though human interference has made recent evolution unnatural for at least a century. Where that trajectory leads, no one can say.

The heart of the dialogue, and the idea most likely to raise eyebrows, concerns what happens underground. Zanella described what he calls a double soil: the familiar one beneath plants, and a second, less visible one inside the bellies of animals, because animals too must digest the food they gather. In both places, pedofauna and microorganisms transform necromass, the dead material of previous generations, into building blocks usable by new life. What emerges is a cyclical process of death and renewal that Zanella suggests we may mistakenly label biodegradation. Death, in this view, is not the end of biological function but its recycling engine, continuously and progressively renewing the soil and enriching the sources of structural building blocks on which every generation depends.

Pignatti pushed the idea further, proposing that small fragments of DNA might travel to new generations outside the known reproductive pathway. DNA exists outside cells, free in the environment or stored in organic matter, like words in a vocabulary accumulated across successive generations. He suggested that such an environmental flow of genetic material could help explain observed co-evolution, the existence of non-coding DNA, and the puzzling presence of DNA belonging to organisms other than the one that houses it, findings documented in the scientific literature of recent decades. Zanella found the notion electrifying: evolution would involve not only sexually transmitted DNA but the genetic traffic of an entire co-inhabiting community, flowing through the soil in confined digestive processes of death and recycling, dynamic, fluid and unpredictable, branching within the limits imposed by the environment and, today more than ever, by humanity.

From there the conversation turned boldly speculative. Zanella noted that when gametes fuse into a single diploid cell, they partially die, and asked whether reproduction itself might be understood as a consequence of cell death, one cell swallowing another to form a new one. Decomposition and reproduction, he suggested, could be two faces of the same process, a perpetuation of the soil’s logic at the cellular scale, with mitosis and meiosis perhaps acting as miniature recycling mechanisms. He even invoked the famous Miller-Urey experiment of 1959, pointing out that the primordial soup from which life emerged could be read as a primordial soil, or even a primordial cell. Pignatti responded with a unifying image: a transmitted language of DNA fragments, a thread connecting all living beings that still eludes us, and a reminder that Darwin arrived at natural selection without knowing anything about DNA at all.

Crucially, the dialogue is not pure speculation. The authors point to a growing body of published research supporting the functional importance of soil processes in evolution. Studies show that soil microorganisms in natural environments can have lower biodiversity indices yet be more biologically and physiologically connected to one another than those in neighboring anthropized ecosystems. Nitrogen fertilization has been shown to significantly reduce soil bacterial diversity, with stronger effects in cropland than in grassland or forest. Polyspecific meadows make better use of environmental resources than monospecific ones, and a single exogenous species can generate an entirely new ecosystem. Microscopic imaging of a single organo-mineral aggregate from an Andosol reveals interdependent flows of minerals and organic matter driven by biological activity that varies with rainfall, each aggregate functioning as a miniature soil. The pattern that emerges is of living beings organized into functional groups, each serving as a cog in a clock-like system, giving transformed resources to others in order to receive modified resources in return.

This functional perspective carries a sober warning. Simply assembling many species together raises biodiversity counts but does not automatically create a functioning system; such artificial assemblages, if allowed to evolve, tend to drift back toward functionally connected configurations. When humans destroy a natural ecosystem, they eliminate a historical web of biological and physicochemical interdependences that is largely unknown and therefore nearly impossible to reconstruct. The authors’ framing recalls the pioneering Gaia-inspired work of Lovelock and Margulis, extending it to the suggestion that species never evolve alone: it is the ecosystems containing them that evolve, with them, within a hierarchy of nested systems from the cell to the universe. On this reading, Homo sapiens may be just one link in the chain, and a species’ so-called finality always recedes into a changing future.

The excursion ended with an object lesson in ecosystem unity. Within a few meters, the Castelporziano forest shifted from an ash woodland with laurel growing on fresh soil over impermeable clay, to an oak woodland of Turkey and Frainetto oaks on sandy, filtering ground, and the entire ecosystem changed with it, soil and vegetation together. Over sandwiches, Zanella asked Pignatti how he had managed the Flora of Italy; the answer, a house full of plant lists in notebooks scattered along the stairs and shelves, and a network of tireless collaborators, was delivered, the author notes, like a hero. The dialogue they recorded is an invitation to reflect on the meaning of life by considering the functional contribution of death, and on the possibility that the spiral of plants, soil, and recycled DNA turns beneath us still, one of nature’s oldest and least understood engines of evolution.

Subject of Research: The role of soil as a living recycling matrix in evolution, DNA flow, and ecosystem function

Article Title: The spiral of plants and soil in the cycle of life

Article References: Zanella, A. (2024). The spiral of plants and soil in the cycle of life. Italian Botanist, 17, 1-11. https://doi.org/10.3897/italianbotanist.17.107071

Image Credits: AI Generated

DOI: 10.3897/italianbotanist.17.107071

Keywords: soil ecology, evolution, phytosociology, humus, DNA recycling, ecosystems, soil biodiversity, vegetation science, Castelporziano, decomposition, Sandro Pignatti, Italian Botanist

The family Moniligastridae, to which the new species belongs, comprises five genera and 193 known species, and its largest genus, Drawida, accounts for 163 of them. These worms are distributed across South, Southeast, and East Asia, where they play significant roles in soil aeration, nutrient cycling, and decomposition. Drawida gisti itself, first described in 1931 from specimens collected in Jinan and Beijing, is an East Asian endemic of considerable ecological importance. Yet, paradoxically, nearly all research on it has been non-taxonomic, focusing on its ecology or physiology rather than on the fundamental question of what, exactly, a Drawida gisti is. Its species boundaries remained poorly understood, and its true diversity was likely severely underestimated.

The research team, working from the Hebei Key Laboratory of Animal Diversity at Langfang Normal University, took an integrative taxonomic approach, the modern gold standard for resolving cryptic species. They collected fresh specimens by hand-sorting and digging at multiple sites: the new species came from Weiyuan Park in Shanhaiguan District, Qinhuangdao, in Hebei Province, while comparison specimens of Drawida gisti gisti were gathered from Mentougou in Beijing, Rizhao and Heze in Shandong Province, and Chengde in Hebei. All specimens were fixed in the field in 95 percent ethanol and later preserved at minus 20 degrees Celsius, ensuring that both anatomical structures and DNA would survive intact for analysis.

Under the microscope, the worms revealed a suite of diagnostic characters that taxonomists use to tell species apart. Drawida xuqini measures 48 to 87 millimeters in length and 4.5 to 7.0 millimeters in diameter, with 160 to 181 segments and a pale pink clitellum spanning segments X to XIII. Its most distinctive internal features include three to five gizzards, M-shaped prostate glands reaching up to 11.6 millimeters in length, and, crucially, a vas deferens that is very short and entirely uncoiled, a trait unique among members of the newly defined species complex. Its penes are thick with a swollen base and a blunt, rounded apex, in contrast to the slender, sharply tapering penes of Drawida gisti gisti. In alcohol, the new species is light gray rather than the reddish brown of its relative.

The molecular work was equally decisive. The team sequenced complete mitochondrial genomes, which measured 14,647 to 14,750 base pairs and contained the typical 37 mitochondrial genes: 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. Notably, the control region was absent in both species examined, mirroring a pattern seen in some members of the related Drawida japonica species complex. Phylogenetic trees built from the concatenated 13 protein-coding genes, using both maximum-likelihood and Bayesian inference methods, placed the four sequenced individuals of Drawida xuqini together as a distinct, robustly supported lineage, with maximum-likelihood bootstrap support of 100 and a Bayesian posterior probability of 1.00. The two major species complexes, DiSC and DjSC, each formed independent well-supported monophyletic groups.

Genetic distances sealed the case. Using the Kimura two-parameter model on the mitochondrial COI barcode gene, the researchers found that divergence between Drawida xuqini and Drawida gisti gisti ranged from 19.4 to 22.0 percent, far exceeding the 15 percent interspecific threshold routinely applied in earthworm taxonomy. Within the new species, divergence was a mere 0 to 0.5 percent. Three molecular species delimitation methods, Assemble Species by Automatic Partitioning, the Generalized Mixed Yule Coalescent model, and the multi-locus Bayesian Phylogenetics and Phylogeography approach, all converged on the same conclusion: the Qinhuangdao worms represent a separate species, fully congruent with the morphological evidence.

Establishing the species complex itself was a taxonomic detective story. The team reviewed several morphologically similar species described decades ago from eastern and southwestern China, including Drawida cheni, D. linhaiensis, D. sinica, D. sulcata, and D. syringa, whose type specimens are presumed lost and which could only be assessed from published literature. Because these species share key features with Drawida gisti gisti, such as the presence of a penis and penial chamber, and occur in geographic proximity, the researchers hypothesized they are closely allied and formally grouped them, together with D. gisti gisti, D. anchingiana, and D. gisti nanchangiana, into the Drawida gisti species complex. They also provided an updated redescription of D. gisti gisti based on freshly examined specimens from multiple localities, the first such modern treatment for this long-neglected worm.

Perhaps the most provocative finding concerns variation within Drawida gisti gisti itself. Specimens from different localities showed marked plasticity in body color and size, while their internal anatomy remained highly uniform, a disparity the authors suggest may be environmentally induced. More intriguing still, some specimens from Rizhao displayed divergent penial morphology and COI distances of 4.8 to 5.7 percent from typical populations, and single-locus delimitation methods recovered them as distinct evolutionary lineages. The researchers caution that GMYC is known for excessive lineage splitting, but they note that northern populations may not be simple morphological variants of D. gisti from northward dispersal; they could instead constitute cryptic species or novel taxa awaiting validation through expanded sampling. The team also flagged a cautionary tale for the molecular era: a mitochondrial genome previously published as D. gisti was shown by their phylogeny to actually cluster within the D. japonica species complex, a misidentification likely rooted in the lack of authentic reference sequences.

The discovery of Drawida xuqini at Shanhaiguan, where the Great Wall meets the sea, hints at a broader geographic story. The population may represent a peripheral isolate that diverged through geographic isolation and local adaptation under a different climatic regime. Alternatively, given that allied taxa range widely across eastern China, additional cryptic species may be lurking in the southern portion of the distribution. Both hypotheses, the authors stress, require denser sampling across northern and southern provinces to test. What is already clear is that the Moniligastridae family remains taxonomically poorly resolved and that its actual diversity is likely far higher than current counts suggest.

For soil ecologists and conservation biologists, the implications extend beyond nomenclature. Earthworms are ecosystem engineers whose species identity shapes how soils function, and misidentified species can distort everything from biodiversity surveys to ecological risk assessments. The study demonstrates that morphology alone, especially when external characters are plastic and environmentally influenced, is insufficient for accurate species delimitation in this group. Integrative taxonomy, pairing careful dissection with mitochondrial genomics and coalescent-based species delimitation, offers a path forward. As the case of Drawida xuqini shows, a species can sit unnoticed in a city park for generations, distinguished from its famous relative by a coiled tube, the shape of a prostate gland, and a genome that differs by a fifth. The ground beneath East Asia, it seems, still holds many secrets worth digging for.

Subject of Research: Integrative taxonomy and molecular species delimitation of the Drawida gisti earthworm species complex in China

Article Title: Establishment of the Drawida gisti species complex and description of a new species from northeastern China ( Oligochaeta , Moniligastridae )

Article References: Qiao, S., Li, J., Zhang, Y., Aspe, N. M., & Zhao, H. (2026). Establishment of the Drawida gisti species complex and description of a new species from northeastern China (Oligochaeta, Moniligastridae). ZooKeys, 1293, 327-346. https://doi.org/10.3897/zookeys.1293.204408

Image Credits: AI Generated

DOI: 10.3897/zookeys.1293.204408

Keywords: earthworms, Drawida, Moniligastridae, integrative taxonomy, species delimitation, mitochondrial genome, COI barcode, cryptic species, new species, China, ZooKeys, soil biodiversity

The research team, drawing on more than 120 peer-reviewed field studies published up to June 2023, systematically searched eleven specialized scientific databases alongside Google Scholar to assemble density records for earthworms, enchytraeids, collembolans, and soil mites across the country’s diverse landscapes. After applying strict inclusion criteria and discarding studies with unreliable or insufficient data, 102 publications formed the analytical backbone of the review. The researchers converted all abundance figures to a standardized metric of individuals per square meter, allowing direct comparison across studies that had originally used wildly different sampling methods, from hand sorting to chemical extraction to the Tropical Soil Biology and Fertility protocol.

The geographic picture that emerges is strikingly uneven. Nearly half of all studies concentrated in just three southern states: Rio Grande do Sul accounted for 20 percent of the research, Paraná for 19 percent, and Santa Catarina and São Paulo for 8 percent each. The northern Amazonian states of Amazonas and Pará contributed another 15 percent combined, while the remaining states each hosted less than 4 percent of the studies. This clustering reveals a fundamental mismatch between where soil fauna research happens and where the most intensive agriculture occurs. Brazil’s central and southern regions, where cropping frequencies reach 1.25 to 1.70 cycles per year, are not necessarily the same places where scientists have been counting worms and mites, suggesting that research sites may have been chosen more for their proximity to universities than for their representativeness of Brazil’s agricultural heartland.

When the researchers examined how land use shapes soil organism densities, the four groups told strikingly different stories. Earthworms showed relatively modest variation across natural vegetation, arable fields, and grassland, with average densities of 158, 107, and 134 individuals per square meter respectively. Springtails, by contrast, reached their highest average abundance in arable fields at 18,660 individuals per square meter, though this figure was heavily inflated by outlier studies; once those were excluded, natural cover sites supported the highest springtail densities at 3,143 individuals per square meter. Enchytraeids followed a pattern more similar to earthworms, with grassland sites averaging 13,154 individuals per square meter but natural cover and arable land showing substantially lower figures. Soil mites defied easy categorization entirely, with some studies reporting densities exceeding 60,000 individuals per square meter in organic-rich arable soils while others found fewer than 500 in comparable settings.

The seasonal dimension added another layer of complexity. Springtails and soil mites both showed clear preferences for the rainy season, with collembolan densities increasing by roughly 158 percent when comparing dry-season to wet-season averages across all studies. In paired comparisons where researchers sampled the same plots in both seasons using identical methods, the rainy-season advantage for springtails persisted at around 46 percent. Earthworms, surprisingly, showed the opposite pattern in the pooled analysis, averaging 202 individuals per square meter in the dry season versus 126 in the rainy season, though direct paired comparisons generally favored the rainy season. Enchytraeids also appeared more abundant in dry conditions overall, but this trend reversed entirely when a single high-density study from an Amazonian research station was excluded from the calculation.

Perhaps the most consequential finding for Brazilian agriculture concerns tillage. In fields where no tillage was practiced, earthworm densities averaged 77 individuals per square meter; where conventional tillage was employed, the figure plummeted to just 26 individuals per square meter. When the analysis was restricted to studies that directly compared tilled and untilled plots within the same fields, the disparity widened further, with no-tillage fields supporting 97 earthworms per square meter against 26 in tilled fields, representing a potential reduction of at least 67 percent. Individual studies reported even steeper declines, with reductions of 72 to 82 percent documented across different seasons and regions. Springtails also declined under tillage in most individual comparisons, with reported decreases ranging from 30 to 70 percent, though the pooled averages were complicated by high variability between studies.

Soil chemistry added further nuance to the picture. Earthworm densities in arable land appeared to increase with rising pH, from around 20 individuals per square meter at pH 4.0 to 4.5 up to 89 individuals per square meter at pH 6.0 to 6.5, yet in grassland the trend reversed, with peak earthworm densities occurring at the more acidic pH range of 4.0 to 5.0. Soil mites showed a tendency toward higher densities at near-neutral pH values between 6.0 and 7.0, though the researchers cautioned that this pattern might be an artifact of study conditions rather than a genuine biological response. Enchytraeids displayed no consistent pH trend at all, with densities varying by more than two orders of magnitude across different studies conducted at similar pH levels but in different Brazilian states.

The review also exposed how dramatically methodological choices can shape apparent ecological patterns. Studies using hand sorting consistently produced different density estimates than those employing the standardized TSBF method or soil core extraction. The timing of sampling, whether during peak growing season or dormant periods, further modulated results. Perhaps most problematically, many density peaks in the compiled dataset could be traced to single studies conducted under unique environmental or agronomic circumstances, such as a coffee plantation with unusually high organic matter or a research station with distinctive soil properties. When the researchers removed these outlier datasets from their analyses, several apparent trends reversed direction entirely, underscoring how fragile the current understanding of Brazilian soil fauna remains.

The researchers frame their findings within the context of Brazil’s ongoing regulatory transformation. Since 2019, the Brazilian Institute of Environment and Renewable Natural Resources has been developing environmental risk assessment frameworks tailored to local conditions, shifting from a hazard-based classification system toward a prospective risk assessment approach for pesticide registration. To establish realistic protection goals for soil organisms under this new framework, regulators need to understand the Normal Operating Range of soil fauna communities in Brazilian landscapes, meaning the natural occurrence and variability of these organisms across different habitats and environmental conditions. The review’s finding that organism densities can vary by up to three orders of magnitude across land uses, soil types, seasons, and farming practices demonstrates that establishing such reference ranges will be far more challenging than in temperate regions where most existing regulatory frameworks were developed.

The study concludes with a call for coordinated action across academia, regulatory bodies, and industry to harmonize sampling methodologies, expand research coverage into underserved regions such as the Caatinga and Cerrado biomes, and build the comprehensive understanding of soil biodiversity needed to inform ecosystem service-oriented environmental policy. With soils hosting an estimated 40 to 60 percent of all described species globally, and with Brazil’s 846 million hectares facing mounting pressure from agricultural expansion, the stakes of getting this right extend far beyond the country’s borders. The invisible workers beneath Brazilian fields may hold keys to sustainable food production, carbon sequestration, and water regulation on a planetary scale, but only if researchers can first agree on how to count them.

Subject of Research: Soil biodiversity and the effects of land use, tillage, season, and soil properties on earthworms, enchytraeids, collembolans, and soil mites in Brazil

Article Title: Brazilian soils: A 40-year review on earthworms, enchytraeids, collembolans and soil mites

Article References: Petersen-Silva, R., Ribeiro, F., Ferreira, I., & Ernst, G. (2026). Brazilian soils: A 40-year review on earthworms, enchytraeids, collembolans and soil mites. Neotropical Biology and Conservation, 21(1), 1-29. https://doi.org/10.3897/neotropical.21.e175492

Image Credits: AI Generated

DOI: 10.3897/neotropical.21.e175492

Keywords: soil biodiversity, earthworms, enchytraeids, collembola, soil mites, Brazil, tillage, agriculture, soil pH, organic matter, seasonal variation, ecosystem services

The research was carried out in the Private Natural Heritage Reserve RPPN PROMATA, in São Francisco de Paula, in Rio Grande do Sul, Brazil’s southernmost state, at roughly 900 metres above sea level. The team sampled five randomly chosen points in each habitat, all within 150 metres of one another and no more than four kilometres apart at the furthest distance, on a single day in November 2022. After carefully removing leaf litter, they collected two grams of topsoil from the upper five centimetres at each point, kept the samples on ice, and transported them to the laboratory within six hours to minimise shifts in community composition before DNA extraction.

The molecular work relied on high-throughput sequencing on an Illumina MiSeq platform, with separate primer sets targeting the 16S rRNA gene for bacteria and archaea and the 18S rRNA gene for eukaryotes. Raw sequences were quality filtered and denoised into Amplicon Sequence Variants, or ASVs, using the DADA2 pipeline, and taxonomy was assigned against the SILVA and PR2 reference databases with a confidence threshold of at least 80 percent at the family level. In total, the study identified 247 distinct eukaryotic ASVs, 4,201 bacterial ASVs spanning 30 phyla, and 130 archaeal ASVs, providing one of the most detailed multi-domain snapshots of soil life in this highly endemic region.

The taxonomic portraits of the two habitats diverged most clearly among the eukaryotes. In the forest soil, the phylum Cercozoa dominated the unicellular eukaryotic community, with the group Filosa-Sarcomonadea reaching 55.1 percent relative abundance, whereas in the grassland the parasitic phylum Apicomplexa took over, with the class Gregarinomorphea accounting for 83.9 percent of sequences. Among soil animals, annelid worms dominated most forest sites at 57.1 percent mean relative abundance, while nematodes were far more prevalent in grassland, representing 46.7 percent of identified sequences there compared with just 7.55 percent in the forest. Tardigrades appeared exclusively at one grassland site, and ciliates were entirely absent from grassland samples.

In contrast, the prokaryotic communities looked remarkably similar across the habitat boundary. Bacterial communities in both ecosystems were dominated by the phyla Pseudomonadota, Acidobacteriota and Actinomycetota, which together made up 79.08 percent of relative abundance, with the class Alphaproteobacteria reaching 29.7 percent in forest and 37.5 percent in grassland. Archaeal communities were overwhelmingly dominated by the phylum Thermoproteota, whose class Nitrososphaeria reached 85.1 percent in forest and 87.3 percent in grassland. Notably, the ratio between Alphaproteobacteria and Acidobacteriae, often used as an indicator of soil health, was about 1.40 in forest and 1.93 in grassland, values above one that point to healthy soils in both habitats, likely a benefit of long-term protection from disturbance.

Diversity statistics reinforced the forest’s edge. Using incidence-based rarefaction and Hill numbers, the researchers found that richness and both the Shannon and Simpson diversity indices were significantly higher in the Native Forest across all four organism groups, with non-overlapping 95 percent confidence intervals. The gap was widest for bacteria, whose estimated richness in forest soil was almost three times that of the grassland, the greatest disparity observed among the studied groups. Non-metric multidimensional scaling based on Jaccard distances revealed clear spatial separation between the habitats for unicellular eukaryotes, bacteria and archaea, and a significant, though graphically less tractable, separation for metazoans, confirming high beta diversity between the two systems.

One of the study’s most technically interesting contributions is its use of zeta diversity, a multi-site framework that tracks how many species are shared across increasing numbers of sampling sites, avoiding the bias toward rare species that can distort single beta diversity indices. Unicellular eukaryotes started with roughly 35 shared species and then declined steeply, indicating communities dominated by rare, site-specific taxa. Metazoans began with about 15 shared species and followed a similar abrupt decline, with an exponential regression providing the best fit and suggesting a core of specialised species. Bacteria, by contrast, started with around 650 shared species and declined only moderately in a long-tailed pattern best described by a power law, consistent with their habitat-generalist nature. Archaea began with about 17 shared species and showed steep early declines, hinting at communities of rare or highly specialised, possibly endemic organisms.

Co-occurrence network analysis among eukaryotes revealed two well-structured clusters: one linking rotifers, flatworms and Sagenista, and another connecting nematodes, the class Elardia, Coccidiomorphea and Cercozoa. The significant association between Coccidiomorphea, a group within Apicomplexa, and Nematoda is particularly intriguing, since both may infect overlapping categories of host organisms, although the authors caution that such patterns should be interpreted as exploratory and may reflect shared responses to local micro-environmental conditions rather than direct ecological interactions.

The findings carry broader implications for conservation. Primary forests are increasingly recognised as biodiversity reservoirs whose long-term genetic and functional value cannot be quickly replicated by recovering or secondary forests, and this study adds soil microbes and soil animals to that argument. At the same time, the grassland, often described as an underground or dwarf rainforest because of its massive belowground biomass and evolutionary antiquity, made a substantial contribution to regional diversity despite its comparatively lower within-habitat heterogeneity. The clear separation of communities between the two habitats points to environmental filtering driven by vegetation structure, soil physicochemical properties and microclimatic conditions as the prevailing mechanism shaping these assemblages.

The authors are careful to note the limits of their design. With five replicates per habitat and a single sampling date, the observed patterns should be read as indicative rather than exhaustive, and additional sampling could uncover further rare taxa and refine diversity estimates in such heterogeneous soils. Still, the work delivers a foundational characterisation of two adjacent, well-preserved habitats and demonstrates the value of pairing multi-domain metabarcoding with zeta diversity analysis to capture fine-scale community differentiation. Future studies with larger sample sizes, broader sequencing coverage and longitudinal data will be needed to determine whether these community shifts are driven by localised environmental filters, stochastic drift, or a combination of both, but the message is already clear: protecting a landscape means protecting not just its trees and grasses, but the intricate, largely unseen soil worlds beneath them.

Subject of Research: Soil microbial and metazoan community composition in adjacent preserved Atlantic Forest and Highland Grassland habitats assessed by eDNA metabarcoding

Article Title: Soil microbial community composition in two distinct preserved habitats

Article References: Huber, C. S. R., Huber, L. K., & Utz, L. R. P. (2026). Soil microbial community composition in two distinct preserved habitats. Metabarcoding and Metagenomics, 10, Article e183786. https://doi.org/10.3897/mbmg.10.183786

Image Credits: AI Generated

DOI: 10.3897/mbmg.10.183786

Keywords: soil biodiversity, eDNA metabarcoding, Atlantic Forest, Highland Grassland, microbiome, zeta diversity, bacteria, archaea, Cercozoa, Apicomplexa, Nematoda, conservation

Tropical dry forests are defined by prolonged dry seasons, and although they support exceptionally rich floras, they rank among the most threatened biomes on Earth. In the Americas, which hold roughly 54 percent of the biome’s global area, an estimated 66 percent of the original forest cover has already been lost, with deforestation rates running six times higher than in Asia and Africa. Because these forests grow on fertile soils that are prized for agriculture, they have historically attracted intensive human exploitation, and the remaining fragments suffer widespread degradation and limited legal protection. Yet while the trees of these forests have received considerable attention, the life teeming within the soil itself has remained almost entirely undocumented.

The research team, working at eleven sites distributed from the arid Guajira Peninsula in the north through the inter-Andean valleys of the Cauca and Magdalena rivers to the isolated Patía valley in the south, sampled soils during the dry season between November 2018 and February 2019. Each site consisted of a one-hectare plot subdivided into a 20 by 20 meter sampling grid, yielding sixteen composite soil cores per plot. In total, the researchers collected 176 soil samples for DNA analysis and 44 samples for physicochemical characterization, covering elevations from 19 to 1,180 meters above sea level.

The molecular approach relied on eDNA metabarcoding, a technique that amplifies and sequences taxonomically informative DNA regions extracted directly from environmental samples. The team targeted six genetic markers spanning the tree of life: chloroplast trnL for plants, mitochondrial 16S for insects, mitochondrial 12S for oligochaete worms, ITS1 for fungi, 18S rRNA for eukaryotes, and 16S rRNA for bacteria. Rigorous filtering removed contaminants, PCR chimeras, and tag-jump artifacts, and the sequencing effort ultimately produced nearly 100 million reads representing 94,015 molecular operational taxonomic units across all markers and sites.

The taxonomic composition that emerged paints a vivid picture of drought-adapted life. Bacterial communities were dominated by Actinomycetota, a clade previously associated with dry environments and even desert soils, rather than the Acidobacteriota that typically prevail in wetter tropical forest soils. Among fungi, arbuscular mycorrhizal fungi of the class Glomeromycetes were unusually abundant, consistent with reports that these symbionts reach higher diversity in dry ecosystems than in humid tropical forests. Protists showed an elevated relative abundance of Amoebozoa, a group renowned for its drought resistance, while nematodes were conspicuously rare, echoing earlier observations that tropical soils are depauperate in these worms.

The soil mesofauna told a similar story of dry-adapted specialization. Insects detected in the samples consisted mainly of ants, beetles, and termites, groups known to contribute the bulk of soil arthropod biomass in tropical dry forests. Earthworms dominated the oligochaete marker, but enchytraeids, which are known to be sensitive to drought, were scarce. Intriguingly, the researchers also detected Tubificida, oligochaetes typically found in aquatic ecosystems, some of which form drought-resistant cysts that persist near the soil surface. Even the plant DNA recovered from the soil reflected the biome’s signature flora, with Fabaceae and Euphorbiaceae among the most represented families.

Beyond cataloging who lives in these soils, the study probed what governs their distribution. Using variation partitioning analyses that separated the effects of climate, soil properties, and biogeographic region, the researchers uncovered a fundamental divide between microorganisms and macroorganisms. Microbial alpha and beta diversity were primarily shaped by soil physicochemical conditions and climate, with bacteria proving more sensitive to aridity than fungi. Bacterial diversity increased with humidity but decreased with soil fertility, possibly reflecting the dominance of a few fast-growing copiotrophic taxa in nutrient-rich soils. Fungal diversity, by contrast, was highest in the most arid region, Guajira, a pattern that contrasts with global-scale trends and underscores the distinctive ecology of dry tropical soils.

Macroorganisms followed a different rulebook. Plants, insects, and earthworms displayed marked compositional differences among regions that were only weakly explained by measured environmental variables. Instead, most of their variation was associated with the sampled region itself, reflecting a strong biogeographic structure consistent with isolation by distance. The proportion of variation explained by all tested predictors declined steadily with organism size, from 71 percent in bacteria to just 11 percent in insects. This pattern suggests that larger soil organisms disperse less readily, allowing historical processes such as Andean uplift and the post-Pleistocene fragmentation of dry forest corridors to leave lasting imprints on their regional species pools.

Cross-kingdom co-variation analyses added another layer of complexity. Mantel tests revealed significant correlations in community composition between nearly all pairs of taxonomic groups, even after controlling for environmental dissimilarity and site identity. Associations were strongest among microbial groups, with bacteria and protists showing a correlation of 0.66, hinting at genuine biotic interactions such as bacterivory by protists or competition between bacteria and fungi. Weaker but significant correlations between plants and microbes may reflect the prevalence of Fabaceae, which partner with rhizobial bacteria, as well as the influence of plant litter chemistry on decomposer communities.

The implications for conservation are substantial. Because no single taxonomic group can serve as a reliable proxy for the rest of the soil community, restoration and management plans built solely on plant surveys will miss critical dimensions of belowground biodiversity. The study also establishes a vital baseline against which the effects of land-use change and restoration actions can be measured in these fragile environments. As tropical dry forests continue to vanish faster than almost any other tropical biome, understanding the invisible ecosystems beneath their roots may prove just as urgent as protecting the trees themselves, and environmental DNA offers a powerful new lens through which to do so.

Subject of Research: Soil biodiversity and its biogeographic drivers in Colombian tropical dry forests

Article Title: Biogeography of tropical dry forest soils

Article References: Raynaud, J., Calderón-Sanou, I., Gonzalez, M., Baena-Bejarano, N., Chave, J., Donald, J., González-M, R., Iribar, A., Montoya, P., Norden, N., Rodríguez Buriticá, S., Schimann, H., Suescun Darias, U., & Zinger, L. (2026). Biogeography of tropical dry forest soils. Frontiers of Biogeography, 19, Article e182141. https://doi.org/10.21425/fob.19.182141

Image Credits: AI Generated

DOI: 10.21425/fob.19.182141

Keywords: tropical dry forest, soil biodiversity, environmental DNA, metabarcoding, biogeography, Colombia, microbiome, soil mesofauna, aridity, conservation, fungi, bacteria