Genomic insights into key mechanisms for carbon, nitrogen, and phosphate assimilation by the acidophilic, halotolerant genus Acidihalobacter members.

IF 3.5 3区 生物学 Q2 MICROBIOLOGY FEMS microbiology ecology Pub Date : 2024-11-04 DOI:10.1093/femsec/fiae145
Himel Nahreen Khaleque, Homayoun Fathollahzadeh, Anna H Kaksonen, Jorge Valdés, Eva Vergara, David S Holmes, Elizabeth L J Watkin
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Abstract

In-depth comparative genomic analysis was conducted to predict carbon, nitrogen, and phosphate assimilation pathways in the halotolerant, acidophilic genus Acidihalobacter. The study primarily aimed to understand how the metabolic capabilities of each species can determine their roles and effects on the microbial ecology of their unique saline and acidic environments, as well as in their potential application to saline water bioleaching systems. All four genomes encoded the genes for the complete tricarboxylic acid cycle, including 2-oxoglutarate dehydrogenase, a key enzyme absent in obligate chemolithotrophic acidophiles. Genes for a unique carboxysome shell protein, csoS1D, typically found in halotolerant bacteria but not in acidophiles, were identified. All genomes contained lactate and malate utilization genes, but only Ac. ferrooxydans DSM 14175T contained genes for the metabolism of propionate. Genes for phosphate assimilation were present, though organized differently across species. Only Ac. prosperus DSM 5130T and Ac. aeolianus DSM 14174T genomes contained nitrogen fixation genes, while Ac. ferrooxydans DSM 14175T and Ac. yilgarnensis DSM 105917T possessed genes for urease transporters and respiratory nitrate reductases, respectively. The findings suggest that all species can fix carbon dioxide but can also potentially utilize exogenous carbon sources and that the non-nitrogen-fixing species rely on alternative nitrogen assimilation mechanisms.

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从基因组学角度了解嗜酸性耐卤酸杆菌属成员碳、氮和磷酸盐同化的关键机制。
研究人员进行了深入的基因组比较分析,以预测耐盐、嗜酸的酸杆菌属(Acidihalobacter)的碳、氮和磷酸盐同化途径。这项研究的主要目的是了解每个物种的代谢能力如何决定它们在独特的盐酸环境中对微生物生态学的作用和影响,以及它们在盐水生物沥滤系统中的潜在应用。所有四个基因组都编码了完整的三羧酸循环基因,包括 2-氧代戊二酸脱氢酶,这是嗜化石酸性生物所缺乏的一种关键酶。还发现了一种独特的羧酶体外壳蛋白 csoS1D 的基因,这种基因通常存在于耐卤细菌中,但不存在于嗜酸细菌中。所有基因组都包含乳酸和苹果酸利用基因,但只有 Ac. ferrooxydans DSM 14175T 包含丙酸代谢基因。磷酸盐同化基因也存在,但不同物种的组织方式不同。只有 Ac. prosperus DSM 5130T 和 Ac. aeolianus DSM 14174T 的基因组含有固氮基因,而 Ac. ferrooxydans DSM 14175T 和 Ac. yilgarnensis DSM 105917T 则分别含有脲酶转运体和呼吸硝酸还原酶基因。研究结果表明,所有物种都能固定二氧化碳,但也有可能利用外源碳源,而非固氮物种则依赖于其他氮同化机制。
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来源期刊
FEMS microbiology ecology
FEMS microbiology ecology 生物-微生物学
CiteScore
7.50
自引率
2.40%
发文量
132
审稿时长
3 months
期刊介绍: FEMS Microbiology Ecology aims to ensure efficient publication of high-quality papers that are original and provide a significant contribution to the understanding of microbial ecology. The journal contains Research Articles and MiniReviews on fundamental aspects of the ecology of microorganisms in natural soil, aquatic and atmospheric habitats, including extreme environments, and in artificial or managed environments. Research papers on pure cultures and in the areas of plant pathology and medical, food or veterinary microbiology will be published where they provide valuable generic information on microbial ecology. Papers can deal with culturable and non-culturable forms of any type of microorganism: bacteria, archaea, filamentous fungi, yeasts, protozoa, cyanobacteria, algae or viruses. In addition, the journal will publish Perspectives, Current Opinion and Controversy Articles, Commentaries and Letters to the Editor on topical issues in microbial ecology. - Application of ecological theory to microbial ecology - Interactions and signalling between microorganisms and with plants and animals - Interactions between microorganisms and their physicochemical enviornment - Microbial aspects of biogeochemical cycles and processes - Microbial community ecology - Phylogenetic and functional diversity of microbial communities - Evolutionary biology of microorganisms
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Genomic insights into key mechanisms for carbon, nitrogen, and phosphate assimilation by the acidophilic, halotolerant genus Acidihalobacter members. Ecological processes shaping highly connected bacterial communities along strong environmental gradients. Frankia [NiFe] uptake hydrogenases and genome reduction: different lineages of loss. Pollution gradients shape microbial communities associated with Ae. albopictus larval habitats in urban community gardens. The role of family and environment in determining the skin bacterial communities of captive aquatic frogs, Xenopus laevis.
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