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Background Environmental resistomes include transferable microbial genes. One important resistome component is resistance to arsenic, a ubiquitous and toxic metalloid that can have negative and chronic consequences for human and animal health. The distribution of arsenic resistance and metabolism genes in the environment is not well understood. However, microbial communities and their resistomes mediate key transformations of arsenic that are expected to impact both biogeochemistry and local toxicity. Results We examined the phylogenetic diversity, genomic location (chromosome or plasmid), and biogeography of arsenic resistance and metabolism genes in 922 soil genomes and 38 metagenomes. To do so, we developed a bioinformatic toolkit that includes BLAST databases, hidden Markov models and resources for gene-targeted assembly of nine arsenic resistance and metabolism genes: acr3 , aioA , arsB , arsC (grx), arsC (trx), arsD , arsM , arrA , and arxA . Though arsenic-related genes were common, they were not universally detected, contradicting the common conjecture that all organisms have them. From major clades of arsenic-related genes, we inferred their potential for horizontal and vertical transfer. Different types and proportions of genes were detected across soils, suggesting microbial community composition will, in part, determine local arsenic toxicity and biogeochemistry. While arsenic-related genes were globally distributed, particular sequence variants were highly endemic (e.g., acr3 ), suggesting dispersal limitation. The gene encoding arsenic methylase arsM was unexpectedly abundant in soil metagenomes (median 48%), suggesting that it plays a prominent role in global arsenic biogeochemistry. Conclusions Our analysis advances understanding of arsenic resistance, metabolism, and biogeochemistry, and our approach provides a roadmap for the ecological investigation of environmental resistomes.

Nitrous oxide (N 2 O) generation during composting not only leads to losses of nitrogen (N) but also reduces the agronomic values and environmental benefits of composting. This study aimed to investigate the effect of the C/N ratio on N 2 O emissions and its underlying mechanisms at the genetic level during the composting of vegetable waste. The experiment was set up with three treatments, including low C/N treatment (LT, C/N = 18), middle C/N treatment (MT, C/N = 30), and high C/N treatment (HT, C/N = 50). The results showed that N 2 O emission was mainly concentrated in the cooling and maturation periods, and the cumulative N 2 O emissions decreased as the C/N ratio increased. Specifically, the cumulative N 2 O emission was 57,401 mg in LT, significantly higher than 2155 mg in MT and 1353 mg in HT. Lowering the C/N ratio led to increasing TN, NH 4 + -N, and NO 3 − -N contents throughout the composting process. All detected nitrification-related gene abundances in LT continued to increase during composting, significantly surpassing those in MT during the cooling period. By contrast, in HT, there was a slight increase in the abundance of detected nitrification-related genes but a significant decrease in the abundance of narG , napA , and norB genes in the thermophilic and cooling periods. The structural equation model revealed that hao and nosZ genes were vital in N 2 O emissions. In conclusion, increasing the C/N ratio effectively contributed to N 2 O reduction during vegetable waste composting.

Salvia is a large genus with hundreds of species used in traditional Chinese medicine. Tanshinones are a highly representative class of exclusive compounds found in the Salvia genus that exhibit significant biological activity. Tanshinone components have been identified in 16 Salvia species. The CYP76AH subfamily (P450) is crucial for the synthesis of tanshinone due to its catalytic generation of polyhydroxy structures. In this study, a total of 420 CYP76AH genes were obtained, and phylogenetic analysis showed their clear clustering relationships. Fifteen CYP76AH genes from 10 Salvia species were cloned and studied from the perspectives of evolution and catalytic efficiency. Three CYP76AHs with significantly improved catalytic efficiency compared to SmCYP76AH3 were identified, providing efficient catalytic elements for the synthetic biological production of tanshinones. A structure–function relationship study revealed several conserved residues that might be related to the function of CYP76AHs and provided a new mutation direction for the study of the directed evolution of plant P450.

Background and aims Exploring biodiversity linkages between aboveground and belowground biota is a core topic in ecology, and can have implications on our understanding of ecosystem process stability. Yet, this topic still remains underexplored. Here, we explored diversity linkages, in terms of both alpha- and beta-diversity, between plant and top soil microbial communities in a semi-arid grassland ecosystem. Methods Soil microbial community structure was assessed based on both 16S rRNA and functional genes, and plant community composition was evaluated by traditional \"species composition\" and a newly-defined \"biomass composition\", which includes the information on the biomass of each species. Results The bacterial alpha-diversity, expressed as the richness and Shannon diversity of 16S rRNA genes, was significantly correlated with plant species richness and Shannon diversity, whereas the alpha-diversity of microbial functional genes showed marginal association with total plant biomass. Microbial beta-diversity, evaluated by 16S rRNA genes, showed close relationship with plant beta-diversity estimated by both \"species composition\" and \"biomass composition\", while the microbial beta-diversity based on functional genes was only associated with the compositional variation in aboveground plant biomass. Conclusions These results showed that the differences in metabolic potential of soil microbial communities, which is closely related with ecosystem functions, can be better predicted by the variation of plant-derived resources returned to soil, than merely by the species composition of the macro-organism communities.

To compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of China. GeoChip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. Our results indicated that the overall microbial community structures were distinct in each oil-contaminated field, and samples were clustered by geographic locations. The organic contaminant degradation genes were most abundant in all samples and presented a similar pattern under oil contaminant stress among the five fields. In addition, alkane and aromatic hydrocarbon degradation genes such as monooxygenase and dioxygenase were detected in high abundance in the oil-contaminated fields. Canonical correspondence analysis indicated that the microbial functional patterns were highly correlated to the local environmental variables, such as oil contaminant concentration, nitrogen and phosphorus contents, salt and pH. Finally, a total of 59% of microbial community variation from GeoChip data can be explained by oil contamination, geographic location and soil geochemical parameters. This study provided insights into the in situ microbial functional structures in oil-contaminated fields and discerned the linkages between microbial communities and environmental variables, which is important to the application of bioremediation in oil-contaminated sites.

Background The invasiveness of Spartina alterniflora Loisel. into the estuarine coastal wetlands has impacted the stability of soil organic carbon, as well as the functional genes of soil microorganisms. However, the mechanisms by which S. alterniflora invasion affects soil organic carbon, especially at the micro-level, is still unclear. Therefore, this study compared the differences in soil carbon cycling (C-cycling) functional genes between invaded and native areas during the cold season, as well as the changes in microbial communities involved in differential functional genes’ expression. Results Our results showed that in salt marsh wetlands dominated by Suaeda salsa (L.) Pall., invasion by S. alterniflora negatively impacts soil microbial biomass carbon (MBC) and reduces the diversity of C-cycling functional genes. The invasion species significantly increased the relative abundance of carbon fixation genes, while decreasing the relative abundance of carbon degradation genes. Additionally, the differential genes-expressing microbial communities exhibited notable differences across groups. At the class level, both generalist taxa (e.g., Gammaproteobacteria, Deltaproteobacteria) and specialist taxa (e.g., Nitrospiria, Flavobacteriia) collectively influenced the abundance of C-cycling functional genes. Correlation and hierarchical partitioning analyses revealed that the increased soil carbon fixation capacity was closely associated with increased soil organic carbon (SOC) and decreased MBC, whereas the decline in soil carbon degradation capacity was linked to higher soil electrical conductivity (EC) and a lower C:P ratio. Conclusions Our study filled a gap in research during the cold season and revealed that the invasion of S. alterniflora significantly impacts both soil C-cycling functional genes and their expressing microbial communities, thereby potentially affecting the soil organic carbon of salt marsh wetland ecosystems.

Agricultural soils contaminated with heavy metals poison crops and disturb the normal functioning of rhizosphere microbial communities. Different crops and rhizosphere microbial communities exhibit different heavy metal resistance mechanisms. Here, indoor pot studies were used to assess the mechanisms of grain and soil rhizosphere microbial communities on chromium (Cr) stress. Millet grain variety ‘Jingu 21’ ( Setaria italica ) and soil samples were collected prior to control (CK), 6 hours after (Cr_6h), and 6 days following (Cr_6d) Cr stress. Transcriptomic analysis, high-throughput sequencing and quantitative polymerase chain reaction (qPCR) were used for sample determination and data analysis. Cr stress inhibited the expression of genes related to cell division, and photosynthesis in grain plants while stimulating the expression of genes related to DNA replication and repair, in addition to plant defense systems resist Cr stress. In response to chromium stress, rhizosphere soil bacterial and fungal community compositions and diversity changed significantly ( p  < 0.05). Both bacterial and fungal co-occurrence networks primarily comprised positively correlated edges that would serve to increase community stability. However, bacterial community networks were larger than fungal community networks and were more tightly connected and less modular than fungal networks. The abundances of C/N functional genes exhibited increasing trends with increased Cr exposure. Overall, these results suggest that Cr stress primarily prevented cereal seedlings from completing photosynthesis, cell division, and proliferation while simultaneously triggering plant defense mechanisms to resist the toxic effects of Cr. Soil bacterial and fungal populations exhibited diverse response traits, community-assembly mechanisms, and increased expression of functional genes related to carbon and nitrogen cycling, all of which are likely related to microbial survival during Cr stress. This study provides new insights into resistance mechanisms, microbial community structures, and mechanisms of C/N functional genes responses in cereal plants to heavy metal contaminated agricultural soils. Portions of this text were previously published as part of a preprint ( https://www.researchsquare.com/article/rs-2891904/v1 ).

Exploring biodiversity linkages between above-ground and below-ground biota is a core topic in ecology, and can have implications on our understanding of ecosystem process stability. Yet, this topic still remains underexplored. Here, we explored diversity linkages, in terms of both alpha- and beta- diversity, between plant and top soil microbial communities in a semi-arid grassland ecosystem. Soil microbial community structure was assessed based on both 16S rRNA and functional genes, and plant community composition was evaluated by traditional “species composition” and a newly-defined “biomass composition”, which includes the information on the biomass of each species. The bacterial alpha-diversity, expressed as the richness and Shannon diversity of 16S rRNA genes, was significantly correlated with plant species richness and Shannon diversity, whereas the alpha-diversity of microbial functional genes showed marginal association with total plant biomass. Microbial beta-diversity, evaluated by 16S rRNA genes, showed close relationship with plant beta-diversity estimated by both “species composition” and “biomass composition”, while the microbial beta-diversity based on functional genes was only associated with the compositional variation in above-ground plant biomass. These results showed that the differences in metabolic potential of soil microbial communities, which is closely related with ecosystem functions, can be better predicted by the variation of plant-derived resources returned to soil, than merely by the species composition of the macro-organism communities.

Background and aims Phosphorus (P) fertilization affects plant diversity and ecosystem function by changing the abundance and composition of functional soil microorganisms and genes. Understanding the mechanisms regulating the soil carbon (C), nitrogen (N), sulfur (S), and P cycle across different P fertilizer inputs is crucial to the management of P in sustainable agroecosystems. Methods We investigated whether soil functional microorganisms affected the coupling of the abundance of soil C, N, P, and S genes under long-term (up to 14 years) P fertilizer input (0, 21.8, 43.6, and 87.2 kg P ha −1  yr −1 ) on the Loess Plateau of China. Results Long-term P fertilizer input resulted in the increased abundance of soil functional microorganisms and the expression of soil C cycle genes but decreased soil P cycle genes. The relative abundance of ecological clusters (including bacteria, fungi, and archaea) was significantly correlated with functional genes related to the C, N, P, and S cycles. Soil Actinobacteria, Proteobacteria, Cyanobacteria, Bacteroidetes, and Chloroflexi were the keystone taxa mediating soil nutrient cycling in wheat fields. Both Mantel’s test and structural equation modeling indicated that the shifts in soil available C and P were the major factors driving the coupling of soil functional microorganisms and genes. Conclusions The changes in soil microorganisms and genes can drive soil nutrient cycling and promote crop growth, suggesting that their relationship can provide new insight for understanding the microbial mechanisms of soil P turnover in sustainable agroecosystems.

Transcriptomics is one of the most popular topics in biology in recent times. Transcriptome sequencing (RNA-Seq) is a high-throughput, high-sensitivity, and high-resolution technique that can be used to study model and non-model organisms. Transcriptome sequencing is also an important method for studying the genomes of medicinal plants, a topic on which limited information is available. The study of medicinal plants through transcriptomics can help researchers analyze functional genes and regulatory mechanisms of medicinal plants and improve breeding selection and cultivation techniques. This article analyzes and compares the applications of transcriptome sequencing in medicinal plants over the past decade and briefly introduces the methods of transcriptome sequencing and analysis, their applications in medicinal plant research, and potential development trends. We will focus on the research and application progress of transcriptome sequencing in the following four areas: the mining of functional genes in medicinal plants, development of molecular markers, biosynthetic pathways of secondary metabolites, and developmental mechanisms of medicinal plants. Our review will provide ideas for the mining of functional genes of medicinal plants and breeding new varieties.