Reforestation substantially changed the soil antibiotic resistome and its relationships with metal resistance genes, mobile genetic elements, and pathogens

Zhang, Song; Li, Ting; Hu, Jinming; Li, Kexin; Liu, Dong; Li, Haixia; Wang, Fang; Chen, Danhong; Zhang, Zejin; Fan, Qiuping; Cui, Xiaoyong; Che, Rongxiao

doi:10.1016/j.jenvman.2023.118037

Cited by 7 publications

(6 citation statements)

References 87 publications

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“…For example, natural reforestation decreased the diversity of ARGs in soils. 62 Our results suggest that viral communities suppress the earthworm gut antibiotic resistome on a national scale. Viral communities typically have two pathways to affect antibiotic resistomes.…”

Section: Discussionmentioning

confidence: 69%

Viral Communities Suppress the Earthworm Gut Antibiotic Resistome by Lysing Bacteria on a National Scale

Du,

Bi,

Lin

et al. 2024

Environ. Sci. Technol.

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Earthworms are critical in regulating soil processes and act as filters for antibiotic resistance genes (ARGs). Yet, the geographic patterns and main drivers of earthworm gut ARGs remain largely unknown. We collected 52 earthworm and soil samples from arable and forest ecosystems along a 3000 km transect across China, analyzing the diversity and abundance of ARGs using shotgun metagenomics. Earthworm guts harbored a lower diversity and abundance of ARGs compared to soil, resulting in a stronger distance-decay rate of ARGs in the gut. Greater deterministic assembly processes of ARGs were found in the gut than in soil. The earthworm gut had a lower frequency of cooccurrence patterns between ARGs and mobile genetic elements (MGEs) in forest than in arable systems. Viral diversity was higher in the gut compared to soil and was negatively correlated with bacterial diversity. Bacteria such as Streptomyces and Pseudomonas were potential hosts of both viruses and ARGs. Viruses had negative effects on the diversity and abundance of ARGs, likely due to the lysis on ARG-bearing bacteria. These findings provide new insights into the variations of ARGs in the earthworm gut and highlight the vital role of viruses in the regulation of ARGs in the soil ecosystem.

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Section: Discussionmentioning

confidence: 69%

Viral Communities Suppress the Earthworm Gut Antibiotic Resistome by Lysing Bacteria on a National Scale

Du,

Bi,

Lin

et al. 2024

Environ. Sci. Technol.

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“…First, the dispersal of microbes usually occurs by passive mechanisms and strongly depends on the dispersal probability of each microbial taxon (Golan et al, 2017;Nemergut et al, 2013;Zhou & Ning, 2017). Within our study region, the abundance of soil prokaryotes was two orders of magnitude higher than that of fungi (Zhang et al, 2023), resulting in significantly greater passive dispersal opportunities for prokaryotes compared to fungi. Second, the generally smaller cellular sizes of prokaryotes may also contribute to their enhanced dispersal ability.…”

Section: The Assembly Of Soil Prokaryotic and Fungal Communitiesmentioning

confidence: 86%

“…chemoheterotrophs, saprotrophs and ectomycorrhizals) showed high similarities with those of the total prokaryotes and fungi (Figure 6). Additionally, as mentioned above, the generally smaller cellular sizes and higher abundance of prokaryotes, in comparison to fungi, also confer less dispersal limitations on the prokaryotic functional groups (Wang, Zhang, et al, 2017;Zhang et al, 2023). Second, many functional microbes have intimate relationships with their hosts, and thus the subcommunity assembly of some microbial functional groups can be also substantially affected by the hosts (Zhou & Ning, 2017).…”

Section: The Subcommunity Assembly Mechanisms Of Different Microbial ...mentioning

confidence: 98%

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Soil microbial subcommunity assembly mechanisms are highly variable and intimately linked to their ecological and functional traits

Fan,

Liu,

Wang

et al. 2024

Molecular Ecology

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Revealing the mechanisms underlying soil microbial community assembly is a fundamental objective in molecular ecology. However, despite increasing body of research on overall microbial community assembly mechanisms, our understanding of subcommunity assembly mechanisms for different prokaryotic and fungal taxa remains limited. Here, soils were collected from more than 100 sites across southwestern China. Based on amplicon high‐throughput sequencing and iCAMP analysis, we determined the subcommunity assembly mechanisms for various microbial taxa. The results showed that dispersal limitation and homogenous selection were the primary drivers of soil microbial community assembly in this region. However, the subcommunity assembly mechanisms of different soil microbial taxa were highly variable. For instance, the contribution of homogenous selection to Crenarchaeota subcommunity assembly was 70%, but it was only around 10% for the subcommunity assembly of Actinomycetes, Gemmatimonadetes and Planctomycetes. The assembly of subcommunities including microbial taxa with higher occurrence frequencies, average relative abundance and network degrees, as well as wider niches tended to be more influenced by homogenizing dispersal and drift, but less affected by heterogeneous selection and dispersal limitation. The subcommunity assembly mechanisms also varied substantially among different functional guilds. Notably, the subcommunity assembly of diazotrophs, nitrifiers, saprotrophs and some pathogens were predominantly controlled by homogenous selection, while that of denitrifiers and fungal pathogens were mainly affected by stochastic processes such as drift. These findings provide novel insights into understanding soil microbial diversity maintenance mechanisms, and the analysis pipeline holds significant value for future research.

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“…The relative abundance of each functional gene to the 16S rRNA gene copy number was determined using SOAPaligner at a similarity threshold of 95%. The copy number of each functional gene was imputed based on that of the 16S rRNA gene as described in our previous study [44]. The raw metagenomic sequencing data have also been deposited in the NCBI Sequence Read Archive under the BioProject PRJNA1078791.…”

Section: Metagenomic Analysismentioning

confidence: 99%

Coalescence of soil microbial communities: consequences, mechanisms, and influential factors

Chen,

Wang,

Chen

et al. 2024

Preprint

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Background: Community coalescence is a major manner of microbial dispersal and a fundamental process of microbial community assembly, yet little is known about its ecological effects, mechanisms, and influential factors. Here, a series of microcosmic experiments including soil mixing, sterilization, as well as microbial extraction and inoculation, were performed to address the knowledge gaps. Results: We found that most physicochemical and microbial properties of the coalesced soils exhibited intermediate characteristics compared to the original soils. Weighted species additive effect emerged as the primary driver for soil microbial community coalescence, with contributions reaching 58.44% (prokaryotes) and 51.57% (fungi). In contrast, the contributions from environmental selection were only less than 20%. Upon the removal of soil particle barrier effects, the contributions of abiotic and biotic environmental selection to soil microbial community coalescence increased to 34.60% and 23.76%, respectively. However, their interactions substantially offset the main effects of abiotic and biotic environmental selection. Original soil differences, mixing ratios, and priority effects were critical factors affecting the consequences of soil microbial community coalescence. Nevertheless, the mechanisms underlying microbial community coalescence were similar under different mixing ratios. Conclusions: Our findings underscore the predictability of soil microbial community coalescence, providing critical insights into comprehending microbial community assembly mechanisms.

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Reforestation substantially changed the soil antibiotic resistome and its relationships with metal resistance genes, mobile genetic elements, and pathogens

Cited by 7 publications

References 87 publications

Viral Communities Suppress the Earthworm Gut Antibiotic Resistome by Lysing Bacteria on a National Scale

Viral Communities Suppress the Earthworm Gut Antibiotic Resistome by Lysing Bacteria on a National Scale

Soil microbial subcommunity assembly mechanisms are highly variable and intimately linked to their ecological and functional traits

Coalescence of soil microbial communities: consequences, mechanisms, and influential factors

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