Taxa Research Articles

The maxillary palps of Tephritidae are selectively tuned to food volatiles and diverge with ecology

The maxillary palp is an auxiliary olfactory organ in insects, which, different from the antennae, is equipped with only a few olfactory sensory neuron (OSN) types. We postulated that these derived mouthpart structures, positioned at the base of the proboscis, may be particularly important in mediating feeding behaviors. As feeding is spatio-temporally segregated from oviposition in most Tephritidae, this taxonomic group appears quite suitable to parse out sensory breadth and potential functional divergence of palps and antennae. Scanning electron microscopy and anterograde staining underlined the limited palpal olfactory circuit in Tephritidae: only three morphological subtypes of basiconic sensilla were found, each with two neurons, and project to a total of six antennal lobe glomeruli in Bactrocera dorsalis. Accordingly, the palps detected only few volatiles from the headspace of food (fermentation and protein lures) and fruit (guava and mango) compared to the antennae (17 over 77, using gas-chromatography coupled electrophysiology). Interestingly, functionally the antennae were more tuned to fruit volatiles, detecting eight times more fruit than food volatiles (63 over 8), whereas the number of fruit and food volatile detection was more comparable in the palps (14 over 8). As tephritids diverge in oviposition preferences, but converge on food substrates, we postulated that the receptive ranges of palpal circuits would be more conserved compared to the antennae. However, palpal responses of three tephritid species that differed in phylogenetic relatedness and ecologically niche, diverged across ecological rather than phylogenetic rifts. Two species with strongly overlapping ecology, B. dorsalis and Ceratitis capitata, showed inseparable response profiles, whereas the cucurbit specialist Zeugodacus cucurbitae strongly diverged. As Z. cucurbitae is phylogenetically placed between B. dorsalis and C. capitata, the results indicate that ecology overrides phylogeny in the evolution of palpal tuning, in spite of being predisposed to detecting food volatiles.

The role of partner species in the crop cocultures: A meta- analysis

Crop cocultures (the growing of one crop with another plant or animal species as partner) are known to increase yield and other ecosystem services. However, whether and how partner species (i.e., the species grown together with the focal crop) affect coculture effects is poorly understood. Here, we test the effects of partner species using a meta-analysis. Two types of cocultures (i.e., crop-crop and rice-fish cocultures) with 19 cereals as focal crops were considered, and 136 plant or animal species were involved. We found that cocultures increased focal crop yield, the land equivalent ratio and soil organic matter (SOM), and decreased insect pest infestation. Farming practices (i.e., fertilization, pesticide use, and irrigation) did not alter these coculture effects on yield, but fertilization decreased the coculture effect on SOM, and pesticide use reduced the coculture effect on pest control. Without irrigation, cocultures increased yield under drought conditions compared to normal moisture conditions. Beneficial coculture effects were obtained with both plant and animal partner species and under both patterns of partner species grown with focal crops (species addition and species replacement). Functional types of partner plants (i.e., C3, C4, legume and non-legume plants) and taxonomic groups of partner animals (i.e., crabs, fish, shrimps, and turtles) affected coculture effects on yield, SOM, and insect pests. Both multiple functional trait distance and single functional trait distance between the focal crops and plant partners correlated with coculture effect on yield. The results suggest that biological types of partner species are important in obtaining beneficial effects of cocultures.

Evolutionary history and environmental variability structure contemporary tropical vertebrate communities

AbstractAimTropical regions harbour over half of the world's mammals and birds, but how their communities have assembled over evolutionary timescales remains unclear. To compare eco‐evolutionary assembly processes between tropical mammals and birds, we tested how hypotheses concerning niche conservatism, environmental stability, environmental heterogeneity and time‐for‐speciation relate to tropical vertebrate community phylogenetic and functional structure.LocationTropical rainforests worldwide.Time periodPresent.Major taxa studiedGround‐dwelling and ground‐visiting mammals and birds.MethodsWe used in situ observations of species identified from systematic camera trap sampling as realized communities from 15 protected tropical rainforests in four tropical regions worldwide. We quantified standardized phylogenetic and functional structure for each community and estimated the multi‐trait phylogenetic signal (PS) in ecological strategies for the four regional species pools of mammals and birds. Using linear regression models, we test three non‐mutually exclusive hypotheses by comparing the relative importance of colonization time, palaeo‐environmental changes in temperature and land cover since 3.3 Mya, contemporary seasonality in temperature and productivity and environmental heterogeneity for predicting community phylogenetic and functional structure.ResultsPhylogenetic and functional structure showed non‐significant yet varying tendencies towards clustering or dispersion in all communities. Mammals had stronger multi‐trait PS in ecological strategies than birds (mean PS: mammal = 0.62, bird = 0.43). Distinct dominant processes were identified for mammal and bird communities. For mammals, colonization time and elevation range significantly predicted phylogenetic clustering and functional dispersion tendencies respectively. For birds, elevation range and contemporary temperature seasonality significantly predicted phylogenetic and functional clustering tendencies, respectively, while habitat diversity significantly predicted functional dispersion tendencies.Main conclusionsOur results reveal different eco‐evolutionary assembly processes structuring contemporary tropical mammal and bird communities over evolutionary timescales that have shaped tropical diversity. Our study identified marked differences among taxonomic groups in the relative importance of historical colonization and sensitivity to environmental change.

Comparative development of the serotonin- and FMRFamide-immunoreactive components of the nervous system in two distantly related ribbon worm species (Nemertea, Spiralia).

Neurodevelopment in larval stages of non-model organisms, with a focus on the serotonin- and FMRFamide-immunoreactive components, has been in the focus of research in the recent past. However, some taxonomic groups remain understudied. Nemertea (ribbon worms) represent such an understudied clade with only few reports on nervous system development mostly from phylogenetically or developmentally derived species. It would be insightful to explore neurodevelopment in additional species to be able to document the diversity and deduce common patterns to trace the evolution of nervous system development. Fluorescent immunohistochemical labeling with polyclonal primary antibodies against serotonin and FMRF-amide and a monoclonal antibody against synapsin performed on series of fixed larval stages of two nemertean species Cephalothrix rufifrons (Archinemertea, Palaeonemertea) and Emplectonema gracile (Monostilifera, Hoplonemertea) were analyzed with confocal laser scanning microscopy. This contribution gives detailed accounts on the development of the serotonin- and FMRFamide-immunoreactive subsets of the nervous system in two nemertean species from the first appearance of the respective signals. Additionally, data on synapsin-like immunoreactivity illustrates the general structure of neuropil components. Events common to both investigated species are the appearance of serotonin-like immunoreactive signals before the appearance of FMRF-like immunoreactive signals and the strict progression of the development of the lateral nerve cords from the anteriorly located, ring-shaped brain toward the posterior pole of the larva. Notable differences are (1) the proboscis nervous system that is developing much earlier in investigated larval stages of E. gracile and (2) distinct early, but apparently transient, serotonergic neurons on the frontal and caudal pole of the larva in E. gracile that seem to be absent in C. rufifrons. According to the results from this investigation and in line with previously published accounts on nervous system development, the hypothetical last common ancestor of Nemertea had a ring-shaped brain arranged around the proboscis opening, from which a pair of ventro-lateral nerve cords develops in anterior to posterior progression. Early frontal and caudal serotonergic neurons that later degenerate or cease to express serotonin are an ancestral character of Nemertea that they share with several other spiralian clades.

The effect of anaerobic digestate as an organic soil fertilizer on the diversity and structure of the indigenous soil microbial and nematode communities.

Anaerobic digestate is a popular soil additive which can promote sustainability and transition toward a circular economy. This study addresses how anaerobic digestate modifies soil health when combined with a common chemical fertilizer. Attention was given to soil microbes and, a neglected but of paramount importance soil taxonomic group, soil nematodes. A mesocosm experiment was set up in order to assess the soil's microbial and nematode community. The results demonstrated that the microbial diversity was not affected by the different fertilization regimes, although species richness increased after digestate and mixed fertilization. The composition and abundance of nematode community did not respond to any treatment. Mixed fertilization notably increased potassium (K) and boron (B) levels, while nitrate (NO3-) levels were uniformly elevated across fertilized soils, despite variations in nitrogen input. Network analysis revealed that chemical fertilization led to a densely interconnected network with mainly mutualistic relationships which could cause ecosystem disruption, while digestate application formed a more complex community based on bacterial interactions. However, the combination of both orchestrated a more balanced and less complex community structure, which is more resilient to random disturbances, but on the downside, it is more likely to collapse under targeted perturbations.

Response of bacterial and micro-eukaryotic communities to spatio-temporal fluctuations of wastewater in full scale constructed wetlands

How microbial communities respond to wastewater fluctuations is poorly understood. Full-scale surface flow constructed wetlands (SFCWs) were constructed for investigating microbial communities. Results showed that influent wastewater changed sediment bacterial community composition seasonally, indicating that a single bacterial taxonomic group had low resistance (especially, Actinobacteriota and Gammaproteobacteria). However, copy numbers of 16S rRNA, ammonia oxidizing archaea, ammonia oxidizing bacteria, nirS and nirK in the first stage SFCWs were 2.49 × 1010, 3.48 × 109, 5.76 × 106, 8.77 × 108 and 9.06 × 108 g−1 dry sediment, respectively, which remained stable between seasons. Moreover, decreases in the nitrogen concentration in wastewater, changed microbial system state from heterotrophic to autotrophic. Micro-eukaryotic communities were more sensitive to wastewater fluctuations than bacterial communities. Overall, results revealed that microbial communities responded to spatio-temporal fluctuations in wastewater through state changes and species asynchrony. This highlighted complex processes of wastewater treatment by microbial components in SFCWs.

Soil, rhizosphere, and root microbiome in kiwifruit vine decline, an emerging multifactorial disease.

Kiwifruit vine decline syndrome (KVDS) is characterized by severe root system impairment, which leads to irreversible wilting of the canopy. Plants usually collapse rapidly from the appearance of the first aboveground symptoms, without recovery even in the following seasons. The syndrome has been negatively impacting kiwifruit yield in different areas of Italy, the main producing European country, since its first outbreak in 2012. To date, a unique, common causal factor has yet to be found, and the syndrome is referred to as multifactorial. In this article, we investigated the whole biotic community (fungi, bacteria, and oomycetes) associated with the development of KVDS in three different belowground matrices/compartments (soil, rhizosphere, and root). Sampling was performed at both healthy and affected sites located in the main kiwifruit-producing area of Northwestern Italy. To address the multifactorial nature of the syndrome and to investigate the potential roles of abiotic factors in shaping these communities, a physicochemical analysis of soils was also performed. This study investigates the associations among taxonomic groups composing the microbiome and also between biotic and abiotic factors. Dysbiosis was considered as a driving event in shaping KVDS microbial communities. The results obtained from this study highlight the role of the oomycete genus Phytopythium, which resulted predominantly in the oomycete community composition of diseased matrices, though it was also present in healthy ones. Both bacterial and fungal communities resulted in a high richness of genera and were highly correlated to the sampling site and matrix, underlining the importance of multiple location sampling both geographically and spatially. The rhizosphere community associated with KVDS was driven by a dysbiotic process. In addition, analysis of the association network in the diseased rhizosphere revealed the presence of potential cross-kingdom competition for plant-derived carbon between saprobes, oomycetes, and bacteria.

New Caledonian rovers and the historical biogeography of a hyper‐diverse endemic lineage of South Pacific leaf beetles

AbstractSouth Pacific archipelagos are central in the biogeographic debate on the relative importance of vicariance and dispersal in shaping the distribution of species. However, each taxonomic group was subject to different processes and histories, and here, we reveal the historical biogeography of the diverse Eumolpinae leaf beetles, widely distributed in the region. Extensive taxon sampling focusing on South Pacific Eumolpinae was used to infer the first molecular phylogeny of the group using three single‐copy protein‐coding nuclear and two mitochondrial markers. Upon assessing the clade of interest for lineage‐specific variation in substitution rates, the age of the most recent common ancestors was estimated using out‐group calibration and multi‐gamma site models (MGSMs). Biogeographic analyses used standard event‐based inferences also incorporating phylogenetic uncertainty. Zealandian Eumolpinae are monophyletic and appear to have split from their global relatives in the transition from the Cretaceous to the Paleogene. Variation in the rates of molecular evolution affected the in‐group stem branch, with a significant drop in the substitution rate, and the MGSM correction recovered the crown age of Zealandian Eumolpinae during the Late Eocene–Oligocene transition. Biogeographic inference resolved the origin of the radiation in New Caledonia, favouring a null model without island age constraints, and repeated dispersal events to the other islands, including three independent but synchronous colonisations of New Zealand during the Miocene. New Caledonia, with a highly diverse Eumolpinae fauna of uncertain origin, acted as a hub and pump of biodiversity of these beetles in the entire South Pacific region, sending migrants to other islands through long‐distance dispersal with lineages establishing when land became available.

Microporella hastingsae Harmelin, Ostrovsky, Cáceres-Chamizo and Sanner, 2011 (Bryozoa, Cheilostomatida): a possible new Lessepsian species in the Mediterranean Sea?

The introduction of Non-Indigenous Species (NIS) in the Mediterranean Sea is one of the main threats to biodiversity and its increasing frequency could bring a significant ecological impact on native species. However, knowledge of marine bioinvasions, the spreading patterns of NIS and their possible pathways of dispersion is still limited, especially for particular taxonomic groups. In this paper, we report the first Mediterranean record of a colony of a non-indigenous bryozoan, Microporella hastingsae Harmelin, Ostrovsky, Cáceres-Chamizo and Sanner, 2011, found on plastic litter stranded south of Catania (Sicily, western Ionian Sea) during spring 2023. Based on this colony, a formal taxonomic description of M. hastingsae is provided for this species, which was recently erected for old, misidentified material collected in the early twentieth century in the Suez Canal and the north Red Sea. We suggest that the species could be considered a Lessepsian migrant assuming it entered the Mediterranean Sea at any time, through larval dispersal and/or the possible facilitation by human activities, presumably shipping. Further surveys in coastal localities of Sicily and the eastern Mediterranean are needed to confirm the establishment of M. hastingsae or if the present colony only represents an occasional record of the species in the basin.

Insight into the adaptive role of arachnid genome-wide duplication through chromosome-level genome assembly of the Western black widow spider.

Although spiders are one of the most diverse groups of arthropods, the genetic architecture of their evolutionary adaptations is largely unknown. Specifically, ancient genome-wide duplication occurring during arachnid evolution ~450 mya resulted in a vast assembly of gene families, yet the extent to which selection has shaped this variation is understudied. To aid in comparative genome sequence analyses, we provide a chromosome-level genome of the Western black widow spider (Latrodectus hesperus)-a focus due to its silk properties, venom applications, and as a model for urban adaptation. We used long-read and Hi-C sequencing data, combined with transcriptomes, to assemble 14 chromosomes in a 1.46 Gb genome, with 38,393 genes annotated, and a BUSCO score of 95.3%. Our analyses identified high repetitive gene content and heterozygosity, consistent with other spider genomes, whichhas led to challenges in genome characterization. Our comparative evolutionary analyses of eight genomes available for species within the Araneoidea group (orb weavers and their descendants) identified 1,827 single-copy orthologs. Of these, 155 exhibit significant positive selection primarily associated with developmental genes, and with traits linked to sensory perception. These results support the hypothesis that several traits unique to spiders emerged from the adaptive evolution of ohnologs-or retained ancestrally duplicated genes-from ancient genome-wide duplication. These comparative spider genome analyses can serve as a model to understand how positive selection continually shapes ancestral duplications in generating novel traits today within and between diverse taxonomic groups.

Fine-Tuning of DADA2 Parameters for Multiregional Metabarcoding Analysis of 16S rRNA Genes from Activated Sludge and Comparison of Taxonomy Classification Power and Taxonomy Databases.

Taxonomic classification using metabarcoding is a commonly used method in microbiological studies of environmental samples and during monitoring of biotechnological processes. However, it is difficult to compare results from different laboratories, due to the variety of bioinformatics tools that have been developed and used for data analysis. This problem is compounded by different choices regarding which variable region of the 16S rRNA gene and which database is used for taxonomic identification. Therefore, this study employed the DADA2 algorithm to optimize the preprocessing of raw data obtained from the sequencing of activated sludge samples, using simultaneous analysis of three frequently used regions of 16S rRNA (V1-V3, V3-V4, V4-V5). Additionally, the study evaluated which variable region and which of the frequently used microbial databases for taxonomic classification (Greengenes2, Silva, RefSeq) more accurately classify OTUs into taxa. Adjusting the values of selected parameters of the DADA2 algorithm, we obtained the highest possible numbers of OTUs for each region. Regarding biodiversity within regions, the V3-V4 region had the highest Simpson and Shannon indexes, and the Chao1 index was similar to that of the V1-V3 region. Beta-biodiversity analysis revealed statistically significant differences between regions. When comparing databases for each of the regions studied, the highest numbers of taxonomic groups were obtained using the SILVA database. These results suggest that standardization of metabarcoding of short amplicons may be possible.

Effects of Lacticaseibacillus paracasei 327 intake on the intestinal environment in healthy adult Japanese: a randomized, double-blind, placebo-controlled, parallel-group trial

Background: Lacticaseibacillus paracasei 327 (L. paracasei 327) is a lactic acid bacteria isolated from brown rice. It has been reported that sterilized L. paracasei 327 improves bowel movement. Given the reported relationship between intestinal microbiota and bowel movement, we hypothesized that L. paracasei 327 also improves the intestinal environment through its involvement in fluctuations in the composition of the intestinal microbiota. Objective: The purpose of this study was to verify the effects of the consumption of food containing sterilized L. paracasei 327 on the intestinal environment in healthy Japanese adults. Methods: A randomized, double-blind, placebo-controlled, parallel-group trial was conducted in 110 healthy adults aged 20 to 64 years with a defecation frequency of three to five times per week. Participants were divided into two groups, one receiving 25 mg (approximately 5x1010 bacteria) of sterile L. paracasei 327 once daily for two weeks (55 participants) and other receiving placebo for two weeks (55 participants), to test its effect on the intestinal environment. Results: Intestinal microbiota analysis showed that L. paracasei 327 ingestion resulted in a trend towards an increase in Bacteroides and a significant decrease in Clostridium cluster IV in each taxonomic group compared to the placebo group. In addition, for each operational taxonomic units (OTUs), Bacteroides_OTU_469 and Clostridium subcluster XIVa_OTU_754 were significantly increased, and Clostridium cluster IX, Akkermansia_OTU_110 tended to increase, while Clostridium cluster IV_OTU_749 significantly decreased. Furthermore, defecation days and defecation frequency increased significantly. Conclusion: The presumptive species of bacteria in the taxonomic group and OTUs increased by L. paracasei 327 ingestion included short-chain fatty acid-producing bacteria. In addition, Clostridium cluster IV_OTU_749, which was reduced by L. paracasei 327 ingestion, may also be involved in the production of putrefactive products in the intestine. Therefore, these findings suggest that L. paracasei 327 ingestion improves the intestinal environment by increasing short-chain fatty acid-producing bacteria, suppressing putrefactive-producing bacteria, and improving defecation. Trial registration: UMIN000049859 (UMIN-CTR)Keywords: Lactic acid bacteria; Postbiotics; Lacticaseibacillus paracasei 327; Intestinal microbiota; Defecation; Clinical trial

DNA barcoding using chloroplast matK and rbcL regions for the identification of bamboo species in Sabah

Bamboo species play pivotal roles in maintaining ecological diversity and driving socio-economic development in Sabah, Malaysia. However, due to overlapping traits among distinct bamboo species, identifying them based solely on morphological characteristics poses challenges. DNA barcoding emerges as a highly effective method, demonstrating potential accuracy in identifying diverse plant species across various taxa and ecosystems. In this study, we used the chloroplast matK and rbcL regions as barcode markers to identify 15 bamboo plants in Sabah. Both matK and rbcL exhibited a notable 100% accuracy at the genus level, indicating their reliability in capturing broader taxonomic categories during BLAST searches and genetic distance analysis. However, at the species level, the success rate was limited to 60%, revealing challenges in differentiating closely related bamboo species using the existing DNA barcodes. Our findings underscore the need for an advanced DNA barcode reference library with extensive species coverage for accurate species identification. This study not only unveiled crucial insights into bamboo diversity and taxonomy in Sabah but also contributes to ongoing bamboo resource conservation and supports sustainable resource management in the region.

Observations of Weddell seal (Leptonychotes weddellii) supernumerary nipples

A wide variety of nipple locations and configurations exist among pinnipeds. Like all marine mammals, pinnipeds can have supernumerary nipples that form in utero. Supernumerary nipples have been documented in several species of pinnipeds, the only taxonomic group of marine mammals with variation in nipple number. We document multiple observations (n = 4) of female Weddell seals (Leptonychotes weddellii) with supernumerary nipples in Erebus Bay, Antarctica, including a female Weddell seal with four nipples that was observed nursing two pups. Intraspecific variation in the number of supernumerary nipples observed included both one and two supernumerary nipples. The majority of the observed supernumerary nipples were nursed on by pups, but lactation was unable to be confirmed. These are the first documented observations of supernumerary nipples in Weddell seals.

Karyotype Diversification and Chromosome Rearrangements in Squamate Reptiles.

Karyotype diversification represents an important, yet poorly understood, driver of evolution. Squamate reptiles are characterized by a high taxonomic diversity which is reflected at the karyotype level in terms of general structure, chromosome number and morphology, and insurgence of differentiated simple or multiple-sex-chromosome systems with either male or female heterogamety. The potential of squamate reptiles as unique model organisms in evolutionary cytogenetics has been recognised in recent years in several studies, which have provided novel insights into the chromosome evolutionary dynamics of different taxonomic groups. Here, we review and summarize the resulting complex, but promising, general picture from a systematic perspective, mapping some of the main squamate karyological characteristics onto their phylogenetic relationships. We highlight how all the major categories of balanced chromosome rearrangements contributed to the karyotype evolution in different taxonomic groups. We show that distinct karyotype evolutionary trends may occur, and coexist, with different frequencies in different clades. Finally, in light of the known squamate chromosome diversity and recent research advances, we discuss traditional and novel hypotheses on karyotype evolution and propose a scenario of circular karyotype evolution.

A comparison of two gene regions for assessing community composition of eukaryotic marine microalgae from coastal ecosystems

Two gene regions commonly used to characterise the diversity of eukaryotic communities using metabarcoding are the 18S ribosomal DNA V4 and V9 gene regions. We assessed the effectiveness of these two regions for characterising diverisity of coastal eukaryotic microalgae communities (EMCs) from tropical and temperate sites. We binned amplicon sequence variants (ASVs) into the high level taxonomic groups: dinoflagellates, pennate diatoms, radial centric diatoms, polar centric diatoms, chlorophytes, haptophytes and ‘other microalgae’. When V4 and V9 generated ASV abundances were compared, the V9 region generated a higher number of raw reads, captured more diversity from all high level taxonomic groups and was more closely aligned with the community composition determined using light microscopy. The V4 region did resolve more ASVs to a deeper taxonomic resolution within the dinoflagellates, but did not effectively resolve other major taxonomic divisions. When characterising these communities via metabarcoding, the use of multiple gene regions is recommended, but the V9 gene region can be used in isolation to provide high-level community biodiversity to reflect relative abundances within groups. This approach reduces the cost of sequencing multiple gene regions whilst still providing important baseline ecosystem function information.

Children and adults privilege linguistic over visual information when creating comparison classes for prenominal gradable adjectives

Mastering the semantics of gradable adjectives is a complex acquisition task, since their interpretation requires the calculation of a threshold relative to a comparison class. Context plays a role in determining the comparison class in multiple ways; empirical research has focused on non-linguistic cues, such as world knowledge and visual context, and less on linguistic cues, such as the modified head noun. The present study is the first to examine how preschoolers and adults use the taxonomic category encoded by the modified head noun as well as visual cues to interpret relative (big, small) and absolute (clean, dirty) gradable adjectives. Using existing objects from different taxonomic categories (basic-level and superordinate-level), we developed a picture-choice task that allowed us to infer the comparison class and the threshold from participants’ choices. Forty-three children (aged 3 to 5) and 26 adults, all monolingual German-speaking, were tested. Confirming previous research, children, like adults, showed a context-sensitive interpretation of relative but not of absolute gradable adjectives. The taxonomic label was preferred to visual cues in creating the comparison class already by age three; this advantage of linguistic over non-linguistic information was also present in the adults. We explain this finding with the privileged role of information provided by the taxonomic label: the modified head noun encodes the cognitive representation of an object category and the corresponding taxonomic hierarchy. Accordingly, this representation is easily accessible while creating the comparison class, which provides further evidence that language is a powerful tool to modulate our mental computations.

Tree species, mycorrhizal associations, and land-use history as drivers of cohesion in soil biota communities and microbe-fauna interactions

Community cohesion is a recent concept in ecology referring to the varying levels of connectivity and integration between populations of different taxonomic or functional groups within ecosystems. Positive cohesion denotes positive interactions such as mutualism or facilitation, while negative cohesion implies negative interactions such as competitive exclusion or a preference for different habitats. However, the effects of ecosystem characteristics such as tree species identity, mycorrhizal association and land-use history on soil biota community cohesion and microbe-fauna interactions remains poorly understood. We analyzed data on soil microbial biomass and biomass of taxonomic and functional groups of soil fauna obtained from monoculture stands of broadleaved tree species (maple and ash) associated with arbuscular mycorrhiza (AM), broadleaved tree species (beech, lime, and oak) associated with ectomycorrhizal fungi (ECM) and coniferous Norway spruce associated with ECM planted in common garden designs on former cropland and former forest land across Denmark. Our results revealed both positive and negative cohesion within soil communities, with only negative cohesion varying significantly among tree species. Soil biota communities under spruce indicated the most negative cohesion, whereas maple and ash soils showed least negative cohesion. Community cohesion varied across different sampling locations and between sites with different land-use histories. Positive cohesion was more pronounced in former cropland than in former old forest land, while negative cohesion was more pronounced in soils under tree species associated with ECM fungi than in soils beneath tree species associated with AM fungi. Both positive and negative cohesion were strongly influenced by litter chemistry and soil properties, indicating complex ecological dynamics. Soil pH, litter decomposition indices, and soil C:N ratio emerged as key drivers of microbial and faunal community structures. Additionally, the total microbial and faunal biomass, as well as the community structure of soil microbial and faunal communities, indicated strong positive interactions. Our results have the potential to support forest management by aiding in the selection of suitable tree species to support different groups of soil microbes and fauna, which play crucial role in ecosystem services such as nutrient release and transformation of soil organic matter.

Metazoan zooplankton in the Bay of Biscay: a 16-year record of individual sizes and abundances obtained using the ZooScan and ZooCAM imaging systems

Abstract. This paper presents two metazoan zooplankton datasets obtained by imaging samples collected on the Bay of Biscay continental shelf in spring during the PELGAS (PELagique GAScogne) integrated surveys over the 2004–2019 period. The samples were collected at night with a 200 µm mesh-size WP2 net fitted with a Hydrobios (back-run stop) mechanical flowmeter and hauled vertically from the sea floor to the surface, with the maximum depth set at 100 m when the bathymetry was deeper than this. The first dataset originates from samples collected from 2004 to 2016 and imaged on land with the ZooScan and is composed of 1 153 507 imaged and measured objects. The second dataset originates from samples collected from 2016 to 2019 and imaged onboard the R/V Thalassa with the ZooCAM and is composed of 702 111 imaged and measured objects. The imaged objects are composed of zooplankton individuals, zooplankton pieces, non-living particles and imaging artefacts ranging from 300 µm to 3.39 mm in equivalent spherical diameter which were individually imaged, measured and identified. Each imaged object is geolocated and associated with a station, a survey, a year and other metadata. Each object is described by a set of morphological and grey-level-based features (8 bit encoding, 0 = black, 255 = white), including size, that were automatically extracted from each individual image. Each object was taxonomically identified using the web-based application Ecotaxa with built-in random-forest and CNN-based semi-automatic sorting tools, which was followed by expert validation or correction. The objects were sorted into 172 taxonomic and morphological groups. Each dataset features a table combining metadata and data at individual-object granularity from which one can easily derive quantitative population and community descriptors such as abundances, mean sizes, biovolumes, biomasses and size structure. Each object's individual image is provided along with the data. These two datasets can be used in combination for ecological studies, as the two instruments are interoperable, or they can be used as training sets for ZooScan and ZooCAM users. The data presented here are available at the SEANOE dataportal: https://doi.org/10.17882/94052 (ZooScan dataset, Grandremy et al., 2023c) and https://doi.org/10.17882/94040 (ZooCAM dataset, Grandremy et al., 2023d).

Individual and combined effects of non‐native earthworms and native white‐tailed deer on understorey plant survival, growth and reproduction

Abstract Forests in northeastern North America have undergone dramatic transformations due to losses and gains of species, changes in land use and pollution. Historic stressors combined with new threats of white‐tailed deer and non‐native earthworms are threatening native plant diversity. We developed a transplant approach to gauge the importance of deer and earthworms in allowing understorey species recovery. This approach, instead of censusing existing individuals, avoids problems imposed by past land use, dispersal limitation or climate change. We selected 20 native species in different taxonomic and functional groups, with different palatability to herbivores, different life‐history strategies and a range of plant traits (%N, specific leaf area [SLA]) and our selection included species indicative of primary or secondary forests. Using a 2 × 2 full factorial design, we planted species into fenced and unfenced plots with and without existing earthworm invasions in five secondary hardwood forests. We measured survival, plant growth and reproduction over 4–6 years. Earthworm biomass was associated with increased survival of 13 and decreased survival of five species. Surviving transplants grew taller (eight of 12 species measured) and wider (seven of nine species measured) in earthworm plots but were more likely to be attacked by insects. Excluding deer benefitted most species' survival and growth. Taxonomic class, SLA or foliar N did not affect species sensitivity to deer or earthworms. Synthesis. Secondary forests in our region continue to provide suitable habitat for native species. Earthworms and deer are major structuring forces affecting survival and growth of our transplant species, but their impacts are species‐specific and change over time. We observed poorly recognized indirect negative impacts of deer on many unpalatable species. Taxonomic class and differences in plant traits offered no important insights regarding vulnerability to deer or earthworms. Transplanting native species into secondary forests can succeed in restoring understorey communities, but will require fencing or substantial deer population reductions to be successful long term.