The soil microbial food web revisited with metatranscriptomics - predatory Myxobacteria as keystone taxon?

Abstract

1 1 2 3 4 6 7 8 9 10 Abstract Trophic interactions in the microbial food web of soils are crucial for nutrient and carbon cycling. Traditionally, protozoa are considered the major micropredators of bacteria in soil. However, some prokaryotes, such as Myxobacteria and Bdellovibrio are also famous for bacterivorous life style. Until recently, it was impossible to assess the abundance of pro-and eukaryotic micropredators in soils simultaneously. Using a metatranscriptomic three-domain profiling of small subunit ribosomal RNA we investigated the abundance of bacterivores in 28 datasets from eleven European mineral and organic soils of different climatic zones. In all soils, Myxobacteria comprised a significant proportion from 4 -19% of prokaryotic 16S rRNA transcripts and more than 60% of all bacterivores in most soils. Haliangiaceae and Polyangiaceae were most abundant, while the name-giving Myxococcaceae were barely present. Other bacterial predators like Bdellovibrio were low abundant. AlsoProtozoan micropredator 18S rRNA transcripts, e.g. from Cercozoa, Amoebozoa and Ciliophora, were on average less abundant, especially in mineral soils. Nematodes were even less abundant. In addition, we applied a longitudinal approach to identify bacterivores during beech litter colonisation. Here, Myxobacteria showed preydependent, protozoa-like community dynamics during colonisation. Thus, their broad prey range and high abundance suggests a major influence of Myxobacteria on structuring the prokaryotic community composition in soil, and might warrant their classification as keystone taxon. Our results suggest the presence of an ecologically important "bacterial loop" in soil food webs, independent of protozoa and nematodes.

Both Soil Bacteria and Soil Chemical Property Affected the Micropredator Myxobacterial Community: Evidence from Natural Forest Soil and Greenhouse Rhizosphere Soil

“…Most of the myxobacterial sequences from subtropical and tropical forest soil in this study were uncultured. Our results showed that the abundance of Sorangiineae and Nannocystineae were much higher than that of Cystobacterineae, which is consistent with the results indicated by prokaryotic 16S rRNA transcripts [ 48 ]. The low abundance of Cystobacterineae illustrated by culture-independent methods indicates the biases of the culture-dependent method, because species from Cystobacterineae are frequently isolated [ 49 ].…”

Fertilization changes soil microbiome functioning, especially phagotrophic protists

“…Both groups likely respond to similar changes in their surrounding habitat as shown before (Yao et al, 2011;Wang et al, 2019b). Predatory bacteria prey on a diverse range of bacteria (Morgan et al, 2010;Petters et al, 2018) and therefore reduce Significance levels are denoted with *P < 0.05, **P < 0.01, ***P < 0.001. Standardized total effects (direct plus indirect effects) calculated by the SEM are displayed below the SEM.…”

“…These predatory bacteria are also selective in their prey choice (Morgan et al, 2010), and might therefore promote AOB through preying on their bacterial competitors. A strong positive link between predatory/exoparasitic bacteria with phagotrophic protists might be explained by the fact that both predator groups follow abundances of their main prey: bacteria (Geisen et al, 2018;Petters et al, 2018).…”

Differential response to prey quorum signals indicates predatory range of myxobacteria

“…Despite being considered keystone taxa within microbial communities (Petters et al, 2021), the extent of myxobacterial bacterivory and its contribution to nutrient cycling within microbial food webs remains unknown. These results further demonstrate myxobacterial eavesdropping on prey signaling molecules and provide insight into how responses to exogenous signals might correlate with prey range of myxobacteria.…”