Horizontal Gene Transfer and Ecosystem Function Dynamics

Role of horizontal gene transfer and cooperation in rhizosphere microbiome assembly

Microbes employ a variety of mechanisms, encompassing chemical signaling (e.g., quorum-sensing molecules) and genetic processes like horizontal gene transfer (HGT), to engage in interactions. HGT, in particular, holds a pivotal role as it facilitates the generation of metabolic diversity, thus directly or indirectly influencing microorganisms' interactions and functioning within their habitat. In this study, we investigate the correlations between enhanced metabolic diversity through HGT and cooperative behavior in the rhizosphere. Despite the potential drawbacks of cooperative behavior, which renders it susceptible to exploitation by cheaters based on evolutionary theory, HGT emerges as a mitigating factor. It serves as a valuable and adaptive tool for survival in competitive environments, notably the rhizosphere. By initiating a comprehensive discussion on these processes combined, we anticipate achieving a profound understanding of the rhizosphere microbiome, ultimately enhancing soil microbiology management and the exploitation of this ecological niche.

Quantifying microbial guilds

The ecological role of microorganisms is of utmost importance due to their multiple interactions with the environment. However, assessing the contribution of individual taxonomic groups has proven difficult despite the availability of high throughput data, hindering our understanding of such complex systems. Here, we propose a quantitative definition of guild that is readily applicable to metagenomic data. Our framework focuses on the functional character of protein sequences, as well as their diversifying nature. First, we discriminate functional sequences from the whole sequence space corresponding to a gene annotation to then quantify their contribution to the guild composition across environments. In addition, we identify and distinguish functional implementations, which are sequence spaces that have different ways of carrying out the function. In contrast, we found that orthology delineation did not consistently align with ecologically (or functionally) distinct implementations of the function. We demonstrate the value of our approach with two case studies: the ammonia oxidation and polyamine uptake guilds from the Malaspina circumnavigation cruise, revealing novel ecological dynamics of the latter in marine ecosystems. Thus, the quantification of guilds helps us to assess the functional role of different taxonomic groups with profound implications on the study of microbial communities.

Long-term manure inputs induce a deep selection on agroecosystem soil antibiotic resistome

Although the enrichment of antibiotic resistance genes (ARGs) in diverse organic soils have been explored, understanding of the ecological processes governing the composition of ARGs in long-term organically fertilized soils still remains limited across typical agricultural regions. Thus, the distribution and assembly of ARG profile in three typical agricultural soils (black soil, fluvo-aquic soil, and red soil) under long-term contrasting fertilization regimes (chemical-only vs organic-only) were investigated using high-throughput qPCR (HT-qPCR). The application of organic manure significantly increased the abundance and number of ARGs across soils, as compared to those with chemical fertilizer. Organic manure application enriched the abundance of mobile genetic elements (MGEs), which were positively associated with ARGs. In addition, it is long-term organic fertilizer that enriched the number and abundance of opportunist and specialist ARGs in the fluvo-aquic and red soils, but not black soils. The number and abundance of most generalist ARGs did not change significantly among different fertilization or soil types. The assembly process of the ARG profiles tends to be more deterministic in organically fertilized soils than in chemically fertilized soils. These results suggest that long-term organic fertilizer application may contribute to the persistence and health risk of the soil antibiotic resistomes (especially specialist ARGs).

Impacts of farmland application of antibiotic-contaminated manures on the occurrence of antibiotic residues and antibiotic resistance genes in soil: A meta-analysis study

A meta-analysis of 94 published studies was conducted to explore the impacts of farmland application of antibiotic-contaminated manures on antibiotic concentrations and ARG abundances in manure-amended soil. Forty-nine antibiotics were reported, in which chlortetracycline, oxytetracycline, doxycycline, tetracycline, enrofloxacin, ciprofloxacin and norfloxacin were the most prevalent and had relatively high concentrations. The responses of ARG and mobile genetic element (MGE) abundances to farmland application of antibiotic-contaminated manures varied considerably under different management strategies and environmental settings. On average, compared to unamended treatments, farmland application of antibiotic-contaminated manures significantly increased the total ARG and MGE abundances by 591% and 351%, respectively (P < 0.05). Of all the included ARG classes, the largest increase was found for sulfonamide resistance genes (1121%), followed by aminoglycoside (852%) and tetracycline (763%) resistance genes. Correlation analysis suggested that soil organic carbon (SOC) was significantly negatively correlated with antibiotic concentrations in manured soil (P < 0.05) due to the formation of covalent bonds and nonextractable residues. Soil silt content was significantly positively correlated with antibiotic concentration (P < 0.05), which was attributed to greater sorption capacities. The ARG abundances were significantly positively correlated with soil silt content, antibiotic concentrations, mean annual temperature, SOC, MGEs and soil pH (P < 0.05), suggesting that changes in these factors may shape the ARG profiles. Collectively, these findings advanced our understanding of the occurrence of antibiotics and ARGs in manure-amended soil and potential factors affecting them and will contribute to better management of these contaminants in future agricultural production.

Elevational Gradients Impose Dispersal Limitation on Streptomyces

Dispersal governs microbial biogeography, but the rates and mechanisms of dispersal remain poorly characterized for most microbial taxa. Dispersal limitation is driven by limits on dissemination and establishment, respectively. Elevation gradients create striking patterns of biogeography because they produce steep environmental gradients at small spatial scales, and these gradients offer a powerful tool to examine mechanisms of dispersal limitation. We focus on Streptomyces, a bacterial genus common to soil, by using a taxon-specific phylogenetic marker, the RNA polymerase-encoding rpoB gene. By targeting Streptomyces, we assess dispersal limitation at finer phylogenetic resolution than is possible using whole community analyses. We characterized Streptomyces diversity at local spatial scales (100 to 3,000 m) in two temperate forest sites located in the Adirondacks region of New York State: Woods Lake (<100 m elevation change), and Whiteface Mountain (>1,000 m elevation change). Beta diversity varied considerably at both locations, indicative of dispersal limitation acting at local spatial scales, but beta diversity was significantly higher at Whiteface Mountain. Beta diversity varied across elevation at Whiteface Mountain, being lowest at the mountain’s base. We show that Streptomyces taxa exhibit elevational preferences, and these preferences are phylogenetically conserved. These results indicate that habitat preferences influence Streptomyces biogeography and suggest that barriers to establishment structure Streptomyces communities at higher elevations. These data illustrate that Streptomyces biogeography is governed by dispersal limitation resulting from a complex mixture of stochastic and deterministic processes.

Kaolinite weakens the co-stress of ampicillin and tetracycline on Escherichia coli through multiple pathways

Ampicillin and tetracycline are common antibiotics and can threaten humans by inducing antibiotic resistance in bacteria. Microorganisms are usually exposed to a mixed antibiotic system in the environment. However, there are few researches on the specific regulatory mechanisms of clay on microorganisms under the stress of complex antibiotics. In this study, tandem mass tag-based coupled with two-dimensional liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) was employed to recognize and quantify changes in protein expression of Escherichia coli (E. coli) after culture for 15 days, with or without kaolinite in the co-stress of ampicillin and tetracycline. The results indicated that kaolinite could activate metabolic pathways of E. coli such as the energy metabolism, the biosynthesis of other secondary metabolites, and the metabolism of cofactors and vitamins. Particularly, the fatty acid degradation pathway has also been promoted, indicating that in the same unfavorable environment, kaolinite might influence the composition of E. coli cell membranes. This might be due to the change in membrane composition that was a kind of adaptive strategy of bacterial evolution. Moreover, kaolinite could promote multidrug efflux system to export the bacterial intracellular toxic substances, making E. coli survive better in an adverse environment. Consequently, this study not only disclosed the regulation of kaolinite on E. coli in a complex antibiotic environment but also provided new insights into the environmental process of antibiotic resistance.

Dynamics of the antibiotic resistome in agricultural soils amended with different sources of animal manures over three consecutive years

The application of animal manure is generally considered an important transmission pathway for antibiotic resistance genes (ARGs) in soil. Nevertheless, the fate of ARGs in soil where manure from different sources has been repeatedly implemented is not fully understood. Thus, the succession of ARGs and bacterial communities following the repeated application of three types of animal manures (pig, chicken, and cow manure) to agricultural soil were investigated using Illumina sequencing analysis and high-throughput qPCR. Results showed that manure application remarkably increased the abundance of soil ARGs by increasing the enrichment of indigenous ARGs and introducing extrinsic ARGs. There were no prominent differences in the abundance or diversity of ARGs among the three different manured soils. The abundance and diversity of ARGs in manured soils increased over three consecutive years. Additionally, the abundance of mobile gene elements (MGEs) and bacteria were positively correlated with ARGs, while the changes in the ARG profiles were dramatically associated with the MGEs and bacterial communities. These findings imply that repeated manure application may facilitate to the accumulation and persistence of the soil resistome by regulation of the bacterial community and horizontal gene transfer, providing better insights into the temporal dynamics of soil ARGs in agro-ecosystems.

Profiles of antibiotic resistome with animal manure application in black soils of northeast China

Black soils (Mollisols) are important soil resources for crop production and maintain food safety in China. For keeping soil fertility, the application of animal manure is commonly practiced in black soils. However, the impact of this application on abundance and diversity of antibiotic resistance genes (ARGs) in black soils of China remains unclear. Here, we surveyed the profiles of ARGs in 72 soil samples collected from four long-term experimental stations with different fertilization regimes and from open farmlands in two sites across northeast China using high-throughput quantitative PCR. Results showed that a total of 178 ARGs including mobile genetic elements (MGEs) were detected, and the diversity and abundance of ARGs were significantly increased with manure application. Additionally, the finding of a significant positive correlation between relative abundance of ARGs and MGEs (P <  0.0001), suggesting that horizontal gene transfer may potentially impact the transmission of ARGs. Furthermore, two genes aadA-1-01 and mexF, encoding resistance to aminoglycoside and multidrug, respectively, were recognized as indicators to estimate the abundance of other co-occurring ARGs. These findings provided insights into the soil resistome in black soils of northeast China and also highlighted the environmental risks caused by manure application should not be ignored.

Exploring bacterial functionality in mangrove sediments and its capability to overcome anthropogenic activity

Mangrove forests are highly productive yet vulnerable ecosystems that act as important carbon sinks ("blue carbon"). The objective of this work was to analyze the impact of anthropogenic activities on microbiome structure and functioning. The metagenomic analysis revealed that the taxonomic compositions were grossly similar across all mangrove microbiomes. Remarkably, these microbiomes, along the gradient of anthropogenic impact, showed fluctuations in the relative abundances of bacterial taxa predicted to be involved in sulfur cycling processes. Functions involved in sulfur metabolism, such as APS pathways (associated with sulfate reduction and sulfur oxidation processes) were prevalent across the microbiomes, being sox and dsrAB genes highly expressed on anthropogenically-impacted areas. Apparently, the oil-impacted microbiomes were more affected in taxonomic than in functional terms, as high functional redundancies were noted across them. The microbial gene diversity found was typical for a functional system, even following the previous disturbance.

Dynamical Task Switching in Cellular Computers

We present a scheme for implementing a version of task switching in engineered bacteria, based on the manipulation of plasmid copy numbers. Our method allows for the embedding of multiple computations in a cellular population, whilst minimising resource usage inefficiency. We describe the results of computational simulations of our model, and discuss the potential for future work in this area.

Interaction between typical sulfonamides and bacterial diversity in drinking water

The abuse of antibiotics is becoming more serious as antibiotic use has increased. The sulfa antibiotics, sulfamerazine (SM1) and sulfamethoxazole (SMZ), are frequently detected in a wide range of environments. The interaction between SM1/SMZ and bacterial diversity in drinking water was investigated in this study. The results showed that after treatment with SM1 or SMZ at four different concentrations, the microbial community structure of the drinking water changed statistically significantly compared to the blank sample. At the genus level, the proportions of the different bacteria in drinking water may affect the degradation of the SM1/SMZ. The growth of bacteria in drinking water can be inhibited after the addition of SM1/SMZ, and bacterial community diversity in drinking water declined in this study. Furthermore, the resistance gene sul2 was induced by SM1 in the drinking water.

Environmentally-driven gene content convergence and the Bacillus phylogeny

Background

Members of the Bacillus genus have been isolated from a variety of environments. However, the relationship between potential metabolism and the niche from which bacteria of this genus have been isolated has not been extensively studied. The existence of a monophyletic aquatic Bacillus group, composed of members isolated from both marine and fresh water has been proposed. Here, we present a phylogenetic/phylogenomic analysis to investigate the potential relationship between the environment from which group members have been isolated and their evolutionary origin. We also carried out hierarchical clustering based on functional content to test for potential environmental effects on the genetic content of these bacteria.

Results

The phylogenetic reconstruction showed that Bacillus strains classified as aquatic have evolutionary origins in different lineages. Although we observed the presence of a clade consisting exclusively of aquatic Bacillus, it is not comprised of the same strains previously reported. In contrast to phylogeny, clustering based on the functional categories of the encoded proteomes resulted in groups more compatible with the environments from which the organisms were isolated. This evidence suggests a detectable environmental influence on bacterial genetic content, despite their different evolutionary origins.

Conclusion

Our results suggest that aquatic Bacillus species have polyphyletic origins, but exhibit convergence at the gene content level.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1261-7) contains supplementary material, which is available to authorized users.