Table 1.

Examples for the anthropogenic impact on microbiome signatures in plant holobionts and in terrestrial ecosystems in the Anthropocene from all over the world

Anthropocene signature	Analyzed factor	Ecosystem/holobiont	Resulting microbiome signatures	Reference
Climate change	Global warming	Cropping systems	Warmer temperatures cause an increase of the relative abundance of soil-borne fungal plant pathogens.	[23]
		Cherry	Warming increased the abundance of fungal plant pathogens with higher host infection rates as a consequence.	[24]
		Bog ecosystem	Microbiome shifts were observed in controlled warming experiments. A decreased diversity of bacteria and diazotrophs as well as a reduced nitrogen fixation rate was observed.	[25]
		Oak trees	Increased temperature resulted in lower microbial diversity under controlled conditions. It was also followed by an increase in pathogen occurrence.	[26]
		Grasslands	A decreased ‘drift’ was observed over time, which enhances homogeneous selection that is primarily imposed on Bacillales.	[27]
		Soil leaf litter layer	A short-term adaptation and altered diversity were observed. Non-random, parallel mutations in genes related to nutrient acquisition, stress response, and exopolysaccharide production were characteristic for adaption.	[28]
	Drought	Grasslands	Changes in soil functioning and plant community composition were observed and shown to be shaped via the modification of plant–soil feedbacks under drought conditions.	[29]
		Pine and oak trees	Microbiota shifts and a decrease in diversity were reported.	[30]
	Erosion	Soil	Adaptions were characterized by low microbial network complexity. A decrease in functionality but increase in the relative abundances of some bacterial families involved in N cycling, such as Acetobacteraceae and Beijerinckiaceae was observed.	[31]
Nitrogen and phosphorus flow disturbances	Nitrogen fertilization	Wheat roots and rhizosphere	Overuse of nitrogen fertilizers causes microbiome shifts towards Proteobacteria.	[32]
		Wheat rhizosphere	Bacterial community richness and diversity decreased after plants were supplemented with inorganic nitrogen.	[33]
		Soil	Protist diversity is indirectly reduced by bacterial and fungal community shifts caused by nitrogen inputs in agricultural soils	[34]
		Different forest ecosystems	Nitrogen fertilization substantially reduced the diversity and abundance of nitrogen-fixing bacterial communities under elevated atmospheric CO2 conditions.	[35]
	Phosphorous fertilization	Soil (ryegrass)	One-time inorganic phosphate amendments caused shifts in soil bacterial and fungal communities and reduced mycorrhization rate in ryegrass.	[36]
	Phosphorous and nitrogen fertilization	Barley	Long-term nitrogen fertilization was shown to affect arbuscular mycorrhizal fungal communities while long-term phosphorous fertilization limited phosphorous provision to plants.	[37]
Chemical pollution	Microplastics	Soil	Contamination of different soils with microplastics resulted in a specific enrichment of antibiotic resistance genes. The effect was further enhanced by elevated temperature.	[38]
	Antibiotics, heavy metals, and microplastics	Soil	Enhanced antibiotic resistance occurrence was observed in manured soil.	[39]
	Microplastics	Soil	Altered soil and microbiome structure were liked to microplastics contamination.	[40]
	Neonicotinoid seed treatments	Phyllosphere and soil in soybean-corn agroecosystem	Microbiota shifts were reflected by a decline in the relative abundance of some potentially beneficial soil bacteria (bacteria involved in the N cycle) in response to pesticide applications.	[41]
	Engineered nanomaterials: SiO2, TiO2, and Fe3O4	Maize rhizosphere	A reduction of N-fixing bacteria and iron-redox bacteria was reported along microbiome shifts. Occurrence of plant growth promoting bacteria was enhanced.	[42]
	Broad-spectrum fungicide: N-(3,5-dichlorophenyl) succinimide	Tobacco phyllosphere	Pesticide applications caused a microbiome shift towards a higher prevalence of Gammaproteobacteria in the phyllosphere of treated plants.	[43]
	Antibiotic treatment	Oilseed rape	Mutation frequencies can explain differentiation between plant and clinical Stenotrophomonas maltophilia strains. Clinical environments might select bacterial populations with high mutation frequencies.	[44]
Biodiversity loss	Breeding of high-yield crops	Various crop plants	An overall tendency of microbiome shifts from k- to r-strategists was demonstrated.	[45]
	Breeding of high-yield crops	Maize	It was shown that more recently developed germplasm recruited fewer microbial taxa with the genetic capability for sustainable N provisioning and larger populations of microorganisms that contribute to N losses.	[46]
Stratospheric ozone depletion	UV-B radiation	Peanut phyllopshere	Characterization of 200 phyllosphere isolates indicated that the predominant UV-tolerant members were Bacillus coagulans, Clavibacter michiganensis, and Curtobacterium flaccumfaciens.	[47]
		Maize phyllosphere	UV-B radiation can affect bacterial diversity in the phyllosphere via the host plant’s gene products encoded on identified chromosomal quantitative trait loci (QTL).	[48]
		Maize phyllosphere	A strong tendency toward increased 16S rDNA sequence diversity was observed in UV-exposed samples.	[49]
Combined effects	Agricultural intensification	Various crop plants	A reduced network complexity and a reduced abundance of keystone taxa were described.	[8]
	Diverse	Global microbiome	An enrichment of Firmicutes and hypermutation genes in global microbiomes was observed.	[50]
	Diverse	Soil	Local increase of bacterial diversity and a global-scale homogenization of the soil microbiome was described. Additionally, soil-borne fungal pathogens were shown to accumulate which is accompanied by a reduction of beneficial microbes.	[51]
	Drought and nitrogen availability	Rhizosphere of Alhagi sparsifolia	Rhizospheric fungi are more sensitive to N and water addition than bacteria. Low N input and drought increased microbial co-occurrence network complexity.	[52]