Soil microorganisms, including prokaryotes and eukaryotes, represent a large fraction of global terrestrial biodiversity. These organisms and their microbiomes play critical roles in ecosystem functioning and services and are essential to soil health. Soil biodiversity is governed by above-ground and below-ground factors, which create specific habitat conditions that structure soil communities. However, the compounded effects of such environmental drivers are often understudied, thus limiting our understanding of processes governing soil biodiversity, especially in desert habitats. Here we show that above- and below-ground factors shape prokaryotic and microeukaryotic communities, but these environmental factors do not appear to structure invertebrate-associated microbiomes. By integrating metabarcoding and morphological datasets, we found that soil compactness is a major factor structuring prokaryote and microeukaryote assemblages and influences the abundance of genes involved in nutrient cycling and organic matter decomposition. Despite having lower nitrogen levels, compacted soils displayed significantly higher alpha-diversity than uncompacted habitats across datasets. Different bacterial clades were enriched within specific nematode lineages (Plectids and Tylenchids) highlighting potentially new species-specific nematode-associated taxa. The data suggests that nematode microbiomes are less impacted by the same environmental drivers of the soil bacterial community and respond to microscale variations among sampling sites. The prevalence of functionally diverse invertebrate-associated bacteria (Mycobacterium) in the nematode microbiome suggests that these microbial communities benefit the host. Our findings highlight the importance of assessing above- and below-ground effects to elucidate patterns of microbial community assembly in terrestrial habitats, and how fine-scale analyses are critical for understanding patterns of host-associated microbiomes.

Bloom-forming marine gelatinous zooplankton, including the pelagic tunicate Dolioletta gegenbauri, occur circumglobally and have the potential to significantly influence the structure of pelagic marine food webs and biogeochemical cycling through interactions with microbial communities. Using targeted metabarcoding (16S rRNA genes recovering Bacteria/Archaea) and qPCR approaches associated with laboratory-based feeding experiments, we characterized patterns in doliolid gut microbiomes and microbial communities associated with doliolid fecal pellets and the surrounding seawater. The characterization of starved doliolids provides the first description of the doliolid gut microbiome. At the highest taxonomic levels, doliolid-associated bacterial communities are characteristic of marine bacterioplankton communities around the globe and were dominated by representatives of six major bacterial groups including Gammaproteobacteria, Alphaproteobacteria, Cyanobacteria, Planctomycetes, Bacteroidia and, Phycisphaerae. Comparison between sample types, however, revealed distinct patterns in diversity and biomass supporting the hypothesis that through their presence and trophic activity, doliolids influence the structure of pelagic food webs and biogeochemical cycling in subtropical continental shelf systems where doliolid blooms are common. Bacteria associated with starved doliolids (representative of the resident doliolid gut microbiome) possessed distinct communities, supporting the hypothesis that doliolids possess a unique but low diversity, low biomass microbiome optimized to support a detrital trophic mode. Among potential core microbiome taxa, the genera Pseudoalteromomas and Shimia were the most abundant, similar to patterns observed in other marine invertebrates. Exploratory bioinformatic analyses of predicted functional genes suggest that doliolids, via their interactions with bacterial communities, may affect important biogeochemical processes including nitrogen, sulfur, and organic matter cycling.