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

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]