Slow-moving soil organisms on a water highway: aquatic dispersal and survival potential of Oribatida and Collembola in running water

Community metabarcoding reveals the relative role of environmental filtering and spatial processes in metacommunity dynamics of soil microarthropods across a mosaic of montane forests

Disentangling the relative role of environmental filtering and spatial processes in driving metacommunity structure across mountainous regions remains challenging, as the way we quantify spatial connectivity in topographically and environmentally heterogeneous landscapes can influence our perception of which process predominates. More empirical data sets are required to account for taxon- and context-dependency, but relevant research in understudied areas is often compromised by the taxonomic impediment. Here we used haplotype-level community DNA metabarcoding, enabled by stringent filtering of amplicon sequence variants (ASVs), to characterize metacommunity structure of soil microarthropod assemblages across a mosaic of five forest habitats on the Troodos mountain range in Cyprus. We found similar β diversity patterns at ASV and species (OTU, operational taxonomic unit) levels, which pointed to a primary role of habitat filtering resulting in the existence of largely distinct metacommunities linked to different forest types. Within-habitat turnover was correlated to topoclimatic heterogeneity, again emphasizing the role of environmental filtering. However, when integrating landscape matrix information for the highly fragmented Quercus alnifolia habitat, we also detected a major role of spatial isolation determined by patch connectivity, indicating that stochastic and niche-based processes synergistically govern community assembly. Alpha diversity patterns varied between ASV and OTU levels, with OTU richness decreasing with elevation and ASV richness following a longitudinal gradient, potentially reflecting a decline of genetic diversity eastwards due to historical pressures. Our study demonstrates the utility of haplotype-level community metabarcoding for characterizing metacommunity structure of complex assemblages and improving our understanding of biodiversity dynamics across mountainous landscapes worldwide.

Ecology, genetics and distribution of Punctoribates zachvatkini, an oribatid mite so far overlooked in Germany

Punctoribates is one of few genera in Poronota (Acari: Oribatida) containing species with porose areas and species with saccules, the two types of the octotaxic system. These porose organs are the main difference between two morphologically similar species, P. punctum with porose areas and P. zachvatkini with saccules. As the octotaxic system can vary within species, species separation solely based on this trait might be insufficient. To assess the species status of P. zachvatkini, we investigated additional differences from P. punctum by comparing habitat preferences of the two species regarding nature reserves and agricultural landscapes during a field study in the German Eifel region, and by examining Punctoribates material from four large German natural history museums. We also performed scanning electron microscopy (SEM) and a genetic analysis using the D3 marker of the nuclear 28S rDNA gene. In the field study, P. zachvatkini had higher densities in the nature reserves and P. punctum in the agricultural landscapes. Evaluation of the museum material revealed P. punctum occurred more regularly in disturbed sites such as urban, agricultural and post-mining areas compared to P. zachvatkini. Pairwise distances of the 28S D3 genetic marker as well as an additional base pair in P. zachvatkini further support the separation of the two species, and SEM investigations revealed new details regarding the punctulation of P. zachvatkini. The review of the museum material showed that P. zachvatkini already occurred in Germany in 1967 and has a wider distribution than previously known.

Modelling selection, drift, dispersal and their interactions in the community assembly of Amazonian soil mites

Three processes can explain contemporary community assembly: natural selection, ecological drift and dispersal. However, quantifying their effects has been complicated by confusion between different processes and neglect of expected interactions among them. One possible solution is to simultaneously model the expected effects of each process within species, across communities and across species, thus providing more integrative tests of ecological theory. Here, we used generalized linear mixed models to assess the effects of selection, drift and dispersal on the occurrence probability of 135 soil oribatid mite species across 55 sites over an Amazonian rainforest landscape (64 km²). We tested for interactions between process-related factors and partitioned the explained variation among them. We found that occurrence probability (1) responded to soil P content and litter mass depending on body size and reproductive mode (sexual or parthenogenetic), respectively (selection); (2) increased with community size (drift); and (3) decreased with distance to the nearest source population, and more so in rare species (dispersal limitation). Processes did not interact significantly, and our best model explained 67% of the overall variation in species occurrence probability. However, most of the variation was attributable to dispersal limitation (55%). Our results challenge the seldom-tested theoretical prediction that ecological processes should interact. Rather, they suggest that dispersal limitation overrides the signatures of drift and selection at the landscape level, thus rendering soil microarthropod species ecologically equivalent and possibly contributing to the maintenance of metacommunity diversity.

Wolbachia supergroup E found in Hypochthonius rufulus (Acari: Oribatida) in Poland

Data on the spread of intracellular bacteria in oribatid mites (Acari: Oribatida) are scarce. Our work fills a gap in the research on endosymbionts in this group of invertebrates and provides information on Wolbachia infection in Hypochthonius rufulus (Acari: Oribatida) from soil, litter and moss sample collected in south-eastern Poland. This is the first report of Wolbachia in H. rufulus. Phylogeny based on the analysis of the 16S rRNA, gatB, fbpA, gltA, ftsZ and hcpA gene sequences revealed that Wolbachia from H. rufulus represented supergroup E and was related to bacterial endosymbionts of Collembola. The unique sequence within Wolbachia supergroup E was detected for the 16S rRNA gene of the bacteria from H. rufulus. The sequences of Wolbachia 16S rRNA and housekeeping genes have been deposited in publicly available databases and are an important source of molecular data for comparative studies.

Distinct phylogeographic patterns in populations of two oribatid mite species from the genus Pantelozetes (Acari, Oribatida, Thyrisomidae) in Central Europe

Oribatid mites are important decomposers of dead organic matter in soils across the world. Their origin dates back at least 380 Mya. Multiple severe climatic changes during Late Pliocene and Pleistocene shaped the migration patterns of these organisms and should be reflected in the genetic variability of their current populations. In this study, we examined the genetic diversity and phylogeographic structure as well as the evolutionary history of populations of two ecologically different oribatid mite species. Pantelozetes cavaticus is a troglophile oribatid mite known mainly from Central European caves, whereas Pantelozetes paolii is a common surface eurytopic species with Holarctic distribution. We used two molecular markers-mitochondrial cytochrome c oxidase subunit I (COI) and the nuclear D3 region of the 28S rDNA gene-to reveal phylogenetic relationships between contemporary populations. Whereas the D3 region showed minimal or no variability within populations, COI appeared to be a relevant marker for population studies. Phylogeographic analysis based on COI detected two lineages of P. cavaticus ('Czech' and 'Slovak'), which separated during the Late Pliocene (2.9 Mya) and revealed the existence of one new species. In contrast, three identified genetic lineages of P. paolii (radiation time 2.9 and 1.2 Mya, respectively) uncovered in this study were found to coexist in the distant sampling localities, suggesting a connection between populations even over long distances.

Patterns of intraspecific morphological variability in soil mites reflect their dispersal ability

The ability to disperse is one of the most important factors influencing the biogeography of species and speciation processes. Highly mobile species have been shown to lack geographic population structures, whereas less mobile species show genetically strongly subdivided populations which are expected to also display at least subtle phenotypic differences. Geometric morphometric methods (GMM) were now used to analyze morphological differences between European populations of a presumed non-phoretic, little mobile mite species in comparison to a highly mobile, phoretic species. The non-phoretic species Scutacarus carinthiacus showed a phenotypic population structure, whereas the phoretic species S. acarorum displayed homogeneity. These different patterns most probably can be explained by different levels of gene flow due to different dispersal abilities of the two species. GMM proved to be a sensitive tool that is especially recommendable for the analysis of (old) museum material and/or specimens in microscopic slides, which are not suitable for molecular genetic analysis.

The limited spatial scale of dispersal in soil arthropods revealed with whole-community haplotype-level metabarcoding

Soil arthropod communities are highly diverse and critical for ecosystem functioning. However, our knowledge of spatial structure and the underlying processes of community assembly are scarce, hampered by limited empirical data on species diversity and turnover. We implement a high-throughput sequencing approach to generate comparative data for thousands of arthropods at three hierarchical levels: genetic, species and supra-specific lineages. A joint analysis of the spatial arrangement across these levels can reveal the predominant processes driving the variation in biological assemblages at the local scale. This multihierarchical approach was performed using haplotype-level COI metabarcoding of entire communities of mites, springtails and beetles from three Iberian mountain regions. Tens of thousands of specimens were extracted from deep and superficial soil layers and produced comparative phylogeographic data for >1,000 codistributed species and nearly 3,000 haplotypes. Local assemblage composition differed greatly between grasslands and forests and, within each habitat, showed strong spatial structure and high endemicity. Distance decay was high at all levels, even at the scale of a few kilometres or less. The local distance decay patterns were self-similar for the haplotypes and higher hierarchical entities, and this fractal structure was similar in all regions, suggesting that uniform processes of limited dispersal determine local-scale community assembly. Our results from whole-community metabarcoding provide insight into how dispersal limitations constrain mesofauna community structure within local spatial settings over evolutionary timescales. If generalized across wider areas, the high turnover and endemicity in the soil locally may indicate extremely high richness globally, challenging our current estimations of total arthropod diversity on Earth.

Towards an integrative understanding of soil biodiversity

Soil is one of the most biodiverse terrestrial habitats. Yet, we lack an integrative conceptual framework for understanding the patterns and mechanisms driving soil biodiversity. One of the underlying reasons for our poor understanding of soil biodiversity patterns relates to whether key biodiversity theories (historically developed for aboveground and aquatic organisms) are applicable to patterns of soil biodiversity. Here, we present a systematic literature review to investigate whether and how key biodiversity theories (species-energy relationship, theory of island biogeography, metacommunity theory, niche theory and neutral theory) can explain observed patterns of soil biodiversity. We then discuss two spatial compartments nested within soil at which biodiversity theories can be applied to acknowledge the scale-dependent nature of soil biodiversity.