Soil pH determines arsenic-related functional gene and bacterial diversity in natural forests on the Taibai Mountain

Microbial-driven mechanisms of arsenic methylation during Chinese rice wine fermentation

Arsenic (As) may be a potential contaminant in Chinese rice wine. The methylation of As, which was evaluated as a possible detoxification mechanism to solve this issue. In this study, we simulated Chinese rice wine fermentation under laboratory conditions to explore As methylation behavior. The total As content of Chinese rice wine decreased by 68.6 % after fermentation. As species were transformed during fermentation; inorganic arsenic (iAs) was converted to methylated As; iAs decreased by 73.29 %, and the dimethylarsenic acid (DMA) percentage increased from 4.4 % to 19.9 %. We found that the As methylation gene (arsM) was ubiquitous in Chinese rice wine. Correlation analysis showed that physicochemical properties determined arsM abundance and DMA content during fermentation. The microbial As methylation pathway was summarized based on the annotated As functional genes from the Kyoto Encyclopedia of Genes and Genomes database. Higher relative abundances of glutathione S-transferase and arsC promoted the formation of more trivalent As substrates and further promoted methylation behavior for As detoxification during fermentation. According to the microbial arsM contribution analysis, Mycobacteroides, Rhizopus, and Jimgerdemannia were the primary As methylation microorganisms in Chinese rice wine. These results highlighted the specific As methylation process during fermentation, which could improve the control of As contamination in Chinese rice wines.

Lignin and Peptide Promote the Abundance and Activity of Arsenic Methylation Microbes in Paddy Soils

Rice physiological straighthead disease is induced by microbially mediated arsenic methylation and usually regionally distributed in paddy soils. However, the biogeochemical mechanism underlying the geographic distribution of microbial communities harboring methylating genes (arsM) remains unclear. Herein, we revealed significant (p = 0.001) differences in the arsM communities in different regions of Chinese paddy soils at the continental scale. Moreover, a positive correlation between the diversity of arsM communities and the chemodiversity of soil dissolved organic matter (DOM) was revealed. Among the different DOM components, lignin- and peptide-like DOM are the most important DOM components impacting the abundance and diversity of arsM communities. Metatranscriptomic analyses of 18 selected paddy soil samples revealed that the expression of the arsM gene increased with increasing soil lignin and peptide contents. Compared with the control, the addition of lignin and peptide significantly (p < 0.05) increased the methylated As concentration in the incubated paddy soils. Communities harboring arsM genes belonging to the phyla Chloroflexota, Verrucomicrobiota, Deltaproteobacteria, Thermodesulfobacteriota, and Ignavibacteriota mostly dominated in paddy soils with relatively high lignin and peptide contents. This study highlights the correlation between the diversity of DOM and arsM communities in paddy soils and provides mechanistic information for soil arsenic contamination control and sustainable rice production.

Forest management impacts on soil phosphorus cycling: Insights from metagenomics in Moso bamboo plantations

Bamboo forests are crucial ecosystems and provide essential ecological and economic services in both tropical and subtropical regions. Soil phosphorus (P), a vital nutrient for plant growth, is fundamental to the productivity and health of bamboo forests. However, the microbial mechanisms through which management practices affect soil P processes in bamboo forests remain poorly understood. This study employed metagenomics to examine alterations in microbial P cycling in Moso bamboo plantations under three distinct management conditions. The results revealed that intensive management (M2, annual fertilization, selective harvesting, and understory vegetation removal) significantly increased soil inorganic P (Pi) by 61.76% and 87.39% compared to extensive management (M1, selective bamboo trunk and shoot harvesting every two years) and non-management (M0), respectively, while decreasing soil organic P (Po) by 50.41% and 41.05%. Forest management significantly altered the bacterial communities: Firmicutes, WPS-2, and Acidobacteriales were represented in M2, Xanthobacteraceae in M1, and Chloroflexi AD3, Acidothermus, and Subgroup_2 in M0. M2 significantly increased the community-level habitat niche breadth and weakened the deterministic process of bacterial community assembly relative to M1 and M0 (p ≤ 0.05). Furthermore, functional metagenomics showed that the total abundance of genes related to Po mineralization, P transportation, and P regulation was significantly lower (p ≤ 0.05) in M2 than in M0 and M1. pstA, pstB, and pstC were more abundant in M2 (p ≤ 0.05), whereas phnN, phnI, phnG, phoA, phoD, phnC, phnD, and phnE were more abundant in M1 (p ≤ 0.05), and phnF was significantly abundant in M0 (p ≤ 0.05). A partial least squares path model indicated that soil bacterial community and P cycling genes had direct effects on Pi and Po, respectively. These findings enhance our understanding of the links between forest management practices and P cycling, providing insights for improving soil functionality and nutrient balance.

Various microbial taxa couple arsenic transformation to nitrogen and carbon cycling in paddy soils

BACKGROUND

Arsenic (As) metabolism pathways and their coupling to nitrogen (N) and carbon (C) cycling contribute to elemental biogeochemical cycling. However, how whole-microbial communities respond to As stress and which taxa are the predominant As-transforming bacteria or archaea in situ remains unclear. Hence, by constructing and applying ROCker profiles to precisely detect and quantify As oxidation (aioA, arxA) and reduction (arrA, arsC1, arsC2) genes in short-read metagenomic and metatranscriptomic datasets, we investigated the dominant microbial communities involved in arsenite (As(III)) oxidation and arsenate (As(V)) reduction and revealed their potential pathways for coupling As with N and C in situ in rice paddies.

RESULTS

Five ROCker models were constructed to quantify the abundance and transcriptional activity of short-read sequences encoding As oxidation (aioA and arxA) and reduction (arrA, arsC1, arsC2) genes in paddy soils. Our results revealed that the sub-communities carrying the aioA and arsC2 genes were predominantly responsible for As(III) oxidation and As(V) reduction, respectively. Moreover, a newly identified As(III) oxidation gene, arxA, was detected in genomes assigned to various phyla and showed significantly increased transcriptional activity with increasing soil pH, indicating its important role in As(III) oxidation in alkaline soils. The significant correlation of the transcriptional activities of aioA with the narG and nirK denitrification genes, of arxA with the napA and nirS denitrification genes and of arrA/arsC2 with the pmoA and mcrA genes implied the coupling of As(III) oxidation with denitrification and As(V) reduction with methane oxidation. Various microbial taxa including Burkholderiales, Desulfatiglandales, and Hyphomicrobiales (formerly Rhizobiales) are involved in the coupling of As with N and C metabolism processes. Moreover, these correlated As and N/C genes often co-occur in the same genome and exhibit greater transcriptional activity in paddy soils with As contamination than in those without contamination.

CONCLUSIONS

Our results revealed the comprehensive detection and typing of short-read sequences associated with As oxidation and reduction genes via custom-built ROCker models, and shed light on the various microbial taxa involved in the coupling of As and N and C metabolism in situ in paddy soils. The contribution of the arxA sub-communities to the coupling of As(III) oxidation with nitrate reduction and the arsC sub-communities to the coupling of As(V) reduction with methane oxidation expands our knowledge of the interrelationships among As, N, and C cycling in paddy soils. Video Abstract.

Geochip 5.0 insights into the association between bioleaching of heavy metals from contaminated sediment and functional genes expressed in consortiums

The heavy metal contamination in river and lake sediments endangers aquatic ecosystems. Herein, the feasibility of applying different exogenous mesophile consortiums in bioleaching multiple heavy metal-contaminated sediments from Xiangjiang River was investigated, and a comprehensive functional gene array (GeoChip 5.0) was used to analyze the functional gene expression to reveal the intrinsic association between metal solubilization efficiency and consortium structure. Among four consortiums, the Acidithiobacillus thiooxidans and Leptospirillum ferrooxidans consortium had the highest solubilization efficiencies of Cu, Pb, Zn, and Cd after 15 days, reaching 50.33, 29.93, 47.49, and 79.65%, while Cu, Pb, and Hg had the highest solubilization efficiencies after 30 days, reaching 63.67, 45.33, and 52.07%. Geochip analysis revealed that 31,346 genes involved in different biogeochemical processes had been detected, and the systems of 15 days had lower proportions of unique genes than those of 30 days. Samples from the same stage had more genes overlapping with each other than those from different stages. Plentiful metal-resistant and organic remediation genes were also detected, which means the metal detoxification and organic pollutant degradation had happened with the bioleaching process. The Mantel test revealed that Pb, Zn, As, Cd, and Hg solubilized from sediment influenced the structure of expressed microbial functional genes during bioleaching. This work employed GeoChip to demonstrate the intrinsic association between functional gene expression of mesophile consortiums and the bioleaching efficiency of heavy metal-contaminated sediment, and it provides a good reference for future microbial consortium design and remediation of river and lake sediments.

Nitrogen addition accelerates litter decomposition and arsenic release of Pteris vittata in arsenic-contaminated soil from mine

The arsenic (As) release from litter decomposition of As-hyperaccumulator (Pteris vittata L.) in mine areas poses an ecological risk for metal dispersion into the soil. However, the effect of atmospheric nitrogen (N) deposition on the litter decomposition of As-hyperaccumulator in the tailing mine area remains poorly understood. In this study, we conducted a microcosm experiment to investigate the As release during the decomposition of P. vittata litter under four gradients of N addition (0, 5, 10, and 20 mg N g-1). The N10 treatment (10 mg N g-1) enhanced As release from P. vittata litter by 1.2-2.6 folds compared to control. Furthermore, Streptomyces, Pantoea, and Curtobacterium were found to primarily affect the As release during the litter decomposition process. Additionally, N addition decreased the soil pH, subsequently increased the microbial biomass, as well as hydrolase activities (NAG) which regulated N release. Thereby, N addition increased the As release from P. vittata litter and then transferred to the soil. Moreover, this process caused a transformation of non-labile As fractions into labile forms, resulting in an increase of available As concentration by 13.02-20.16% within the soil after a 90-day incubation period. Our findings provide valuable insights into assessing the ecological risk associated with As release from the decomposition of P. vittata litter towards the soil, particularly under elevated atmospheric N deposition.

The application of mixed stabilizing materials promotes the feasibility of the intercropping system of Gynostemma pentaphyllum/Helianthus annuus L. on arsenic contaminated soil

Intercropping technology and stabilizing materials are common remediation techniques for soils contaminated with heavy metals. This study investigated the feasibility of the Gynostemma pentaphyllum (G. pentaphyllum)/Helianthus annuus L. (H. annuus) intercropping system on arsenic (As) contaminated farmland through field and pot experiments and the regulation of plant As absorption by the application of mixed stabilizing materials in this intercropping system. Field experiments demonstrated that intercropping with H. annuus increased the As concentration in G. pentaphyllum leaves to 1.79 mg kg-1 but still met the requirements of the national food standard of China (2 mg kg-1) (GB2762-2017). Meanwhile, G. pentaphyllum yield in the intercropping system decreased by 15.09%, but the difference was insignificant (P > 0.05). Additionally, the As bioconcentration (BCA) per H. annuus plant in the intercropping system was significantly higher than that in the monoculture system, increasing by 76.37% (P < 0.05). The pot experiment demonstrated that when granite powder, iron sulfate mineral, and "Weidikang" soil conditioner were applied to the soil collectively, G. pentaphyllum leaf As concentration in the intercropping system could be significantly reduced by 42.17%. Rhizosphere pH is the most crucial factor affecting As absorption by G. pentaphyllum in intercropping systems. When these three stabilizing materials were applied simultaneously, the As bioaccumulation (BCA) per H. annuus plant was significantly higher than that of normal intercropping treatment, which increased by 71.12% (P < 0.05), indicating that the application of these stabilizing materials significantly improved the As removal efficiency of the intercropping system. Dissolved organic carbon (DOC) concentration in the rhizosphere soil is the most pivotal factor affecting As absorption by H. annuus. In summary, the G. pentaphyllum-H. annuus intercropping model is worthy of being promoted in moderately As polluted farmland. The application of granite powder, iron sulfate mineral, and "Weidikang" soil conditioner collectively to the soil can effectively enhance the potential of this intercropping model to achieve "production while repairing" in the As polluted farmland.