Thiobacillus spp. and Anaeromyxobacter spp. mediate arsenite oxidation-dependent biological nitrogen fixation in two contrasting types of arsenic-contaminated soils

Li, Yongbin; Guo, Lifang; Yang, Rui; Yang, Zhen; Zhang, Haihan; Li, Qiqian; Cao, Zhiguo; Zhang, Xin; Gao, Pin; Gao, Wenlong; Yan, Geng; Huang, Duanyi; Sun, Weimin

doi:10.1016/j.jhazmat.2022.130220

Cited by 27 publications

(12 citation statements)

References 68 publications

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“…5c ). It has been previously reported that As(III) oxidation can fuel biological nitrogen fixation in tailing and metal(loid)-contaminated soils 55 , 56 . The data present here further complement that diazotrophs could also fix N 2 using energy obtained from dissimilatory As(V) reduction.…”

Section: Resultsmentioning

confidence: 99%

Unexpected genetic and microbial diversity for arsenic cycling in deep sea cold seep sediments

Zhang

Shi

et al. 2023

npj Biofilms Microbiomes

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Cold seeps, where cold hydrocarbon-rich fluid escapes from the seafloor, show strong enrichment of toxic metalloid arsenic (As). The toxicity and mobility of As can be greatly altered by microbial processes that play an important role in global As biogeochemical cycling. However, a global overview of genes and microbes involved in As transformation at seeps remains to be fully unveiled. Using 87 sediment metagenomes and 33 metatranscriptomes derived from 13 globally distributed cold seeps, we show that As detoxification genes (arsM, arsP, arsC1/arsC2, acr3) were prevalent at seeps and more phylogenetically diverse than previously expected. Asgardarchaeota and a variety of unidentified bacterial phyla (e.g. 4484-113, AABM5-125-24 and RBG-13-66-14) may also function as the key players in As transformation. The abundances of As cycling genes and the compositions of As-associated microbiome shifted across different sediment depths or types of cold seep. The energy-conserving arsenate reduction or arsenite oxidation could impact biogeochemical cycling of carbon and nitrogen, via supporting carbon fixation, hydrocarbon degradation and nitrogen fixation. Overall, this study provides a comprehensive overview of As cycling genes and microbes at As-enriched cold seeps, laying a solid foundation for further studies of As cycling in deep sea microbiome at the enzymatic and processual levels.

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Section: Resultsmentioning

confidence: 99%

Unexpected genetic and microbial diversity for arsenic cycling in deep sea cold seep sediments

Zhang

Shi

et al. 2023

npj Biofilms Microbiomes

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“…nifHDK ) were detected in one arxA -carrying (Gammaproteobacteria, n = 1) and six arrA -carrying (Gammaproteobacteria, n = 1; Desulfobacterota, n = 4; Desulfobacterota_I, n = 1) MAGs ( Figure 5c ). It has been previously reported that As(III) oxidation can fuel biological nitrogen fixation in tailing and metal(loid)-contaminated soils 55, 56 . The data present here further complement that diazotrophs could also fix N 2 using energy obtained from dissimilatory As(V) reduction.…”

Section: Resultsmentioning

confidence: 99%

Unexpected genetic and microbial diversity for arsenic cycling in deep sea cold seep sediments

Zhang

Shi

et al. 2022

Preprint

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Cold seeps, where cold hydrocarbon-rich fluid escapes from the seafloor, showed strong enrichment of toxic metalloid arsenic (As). The toxicity and mobility of As can be greatly altered by microbial processes that play an important role in global As biogeochemical cycling. However, a global overview of genes and microbes involved in As transformation at seeps remains to be fully unveiled. Using 87 sediment metagenomes and 33 metatranscriptomes derived from 13 globally distributed cold seeps, we show that As resistance genes (arsM, arsP, arsC1/arsC2, acr3) were prevalent at seeps and more phylogenetically diverse than previously expected. Asgardarchaeota and a variety of unidentified bacterial phyla (e.g. 4484-113, AABM5-125-24 and RBG-13-66-14) may also function as the key players in As transformation. The abundances of As-cycling genes and the compositions of As-associated microbiome shifted across different sediment depths or types of cold seep. The energy-conserving arsenate reduction or arsenite oxidation could impact biogeochemical cycling of carbon and nitrogen, via supporting carbon fixation, hydrocarbon degradation and nitrogen fixation. Overall, this study provides a comprehensive overview of As-cycling genes and microbes at As-enriched cold seeps, laying a solid foundation for further studies of As cycling in deep sea microbiome at the enzymatic and processual levels.

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“…The DNA in the CsCl gradients was extracted as previously described. 42 The proportion of putative phototrophic diazotrophs in each fraction was analyzed by quantifying nif H abundance 53 using the TB Green Premix Ex Taq kit (Takara, Kusatsu, Japan). Based on the qPCR assay, DNA of "heavy" or "light" fractions with the highest nif H abundance (day 49) were subjected to amplicon sequencing of the 16S rRNA gene.…”

Section: ■ Materials and Methodsmentioning

confidence: 99%

“…The change of geochemical conditions caused by ecological restoration of mine tailings affected the diversity and structure of indigenous diazotrophs . Instead of heterotrophic diazotrophs, lithotrophic diazotrophs, which use reduced sulfur or metal(loid)s to fuel nitrogen fixation, dominated in mine tailings as reported previously. − …”

Section: Introductionmentioning

confidence: 99%

Phototrophic Nitrogen Fixation, a Neglected Biogeochemical Process in Mine Tailings?

Li,

Sun,

Yang

et al. 2024

Environ. Sci. Technol.

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Biological nitrogen fixation (BNF) has important ecological significance in mine tailing by contributing to the initial accumulation of nitrogen. In addition to chemolithotrophic and heterotrophic BNF, light may also fuel BNF in oligotrophic mine tailings. However, knowledge regarding the occurrence and ecological significance of this biogeochemical process in mine tailings remains ambiguous. The current study observed phototrophic BNF in enrichment cultures established from three primary successional stages (i.e., original tailings, biological crusts, and pioneer plants) of tailings. Notably, phototrophic BNF in tailings may be more active at vegetation stages (i.e., biological crusts and pioneering plants) than in bare tailings. DNA-stable isotope probing identified Roseomonas species as potential aerobic anoxygenic phototrophs responsible for phototrophic BNF. Furthermore, metagenomic binning as well as genome mining revealed that Roseomonas spp. contained essential genes involved in nitrogen fixation, anoxygenic photosynthesis, and carbon fixation, suggesting their genetic potential to mediate phototrophic BNF. A causal inference framework equipped with the structural causal model suggested that the enrichment of putative phototrophic diazotrophic Roseomonas may contribute to an elevated total nitrogen content during primary succession in these mine tailings. Collectively, our findings suggest that phototrophic diazotrophs may play important roles in nutrient accumulation and hold the potential to facilitate ecological succession in tailings.

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Thiobacillus spp. and Anaeromyxobacter spp. mediate arsenite oxidation-dependent biological nitrogen fixation in two contrasting types of arsenic-contaminated soils

Cited by 27 publications

References 68 publications

Unexpected genetic and microbial diversity for arsenic cycling in deep sea cold seep sediments

Unexpected genetic and microbial diversity for arsenic cycling in deep sea cold seep sediments

Unexpected genetic and microbial diversity for arsenic cycling in deep sea cold seep sediments

Phototrophic Nitrogen Fixation, a Neglected Biogeochemical Process in Mine Tailings?

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