Trophic level drives the host microbiome of soil invertebrates at a continental scale

Abstract

Background Increasing our knowledge of soil biodiversity is fundamental to forecast changes in ecosystem functions under global change scenarios. All multicellular organisms are now known to be holobionts, containing large assemblages of microbial species. Soil fauna is now known to have thousands of species living within them. However, we know very little about the identity and function of host microbiome in contrasting soil faunal groups, across different terrestrial biomes, or at a large spatial scale. Here, we examined the microbiomes of multiple functionally important soil fauna in contrasting terrestrial ecosystems across China. Results Different soil fauna had diverse and unique microbiomes, which were also distinct from those in surrounding soils. These unique microbiomes were maintained within taxa across diverse sampling sites and in contrasting terrestrial ecosystems. The microbiomes of nematodes, potworms, and earthworms were more difficult to predict using environmental data, compared to those of collembolans, oribatid mites, and predatory mites. Although stochastic processes were important, deterministic processes, such as host selection, also contributed to the assembly of unique microbiota in each taxon of soil fauna. Microbial biodiversity, unique microbial taxa, and microbial dark matter (defined as unidentified microbial taxa) all increased with trophic levels within the soil food web. Conclusions Our findings demonstrate that soil animals are important as repositories of microbial biodiversity, and those at the top of the food web harbor more diverse and unique microbiomes. This hidden source of biodiversity is rarely considered in biodiversity and conservation debates and stresses the importance of preserving key soil invertebrates.

Effects of Trophic Level and Land Use on the Variation of Animal Antibiotic Resistome in the Soil Food Web

“…This is because microcosm experiments simplify the microbiome and resistome of soil animals, thus failing to reflect the risk of actual transmission of ARGs under field conditions. Several studies have confirmed that bacterial communities and ARGs are significantly correlated in various environments. ,, In addition, a recent study on the microbiome of soil food webs demonstrated that the diversity of animal bacterial community increases with increasing trophic levels . Therefore, we hypothesized that the variability of animal ARGs in soil food webs is related to their trophic levels.…”

“…For soil animal samples, enough soil was collected in the field and brought to the laboratory for animal separation. More details on the collection of soil and animal samples can be found in a previous literature …”

“…The DNeasy Blood and Tissue Kits (QIAGEN, Dusseldorf, Germany) and FastDNA Spin Kit for Soil (MP Biomedical, California, USA) were selected for animal and soil DNA isolation, respectively, according to the manufacturer’s instructions. Further details are provided in our previous study …”

Does Plant Identity Affect the Dispersal of Resistomes Above and Below Ground?

“…Bacterial genera can specify the classification of bacteria relative to bacterial family level and indicate the function of bacteria in soil ecosystem, so we chose the bacterial genus level as the classification basis. Although there are inaccuracies to some extent in identifying bacterial genera or species, it is still acceptable to analyze the bacterial community at the genus level according to numerous studies. ,, OTUs with the sum representative sequences of all samples of <100 were discarded from the final OTU table. A phylogenetic tree was built by a Fast tree algorithm .…”

“…Soil contamination with antibiotics mainly occurs through sewage, , irrigation, , manure, , and sludge , application to fields resulting in, for example, high levels of oxytetracycline in Chinese soils . It is well-recognized that anthropogenic activities have increased both the diversity and abundance of resistomes in soils, with the potential for spread to humans through above- and below-ground pathways. − Given the global nature of the problem, the World Health Organization has characterized resistomes as a global public health crisis…”