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- Effects of Continuous Straw Returning on Soil Functional Microorganisms and Microbial Communities
- Yunpeng Guan , Meikang Wu , Songhao Che , Shuai Yuan , Xue Yang , Siyuan Li , Ping Tian , Lei Wu , Meiying Yang , Zhihai Wu
- J. Microbiol. 2023;61(1):49-62. Published online January 26, 2023
- DOI: https://doi.org/10.1007/s12275-022-00004-6
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- 9 Citations
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Abstract
- This study examined the changes in soil enzymatic activity, microbial carbon source metabolic diversity, and straw decomposition rates in paddy fields treated with 1, 2, or 3 years of straw returning (SR1–SR3). The soil’s ability to decompose straw and cellulolytic bacteria increased with the number of treatment years (1: 31.9% vs. 2: 43.9% vs. 3: 51.9%, P < 0.05). The numbers of Azotobacter, Nitrobacteria, cellulolytic bacteria, and inorganic phosphate bacteria increased progressively with the numbers of straw returning years. Cellulolytic bacteria and inorganic phosphate bacteria were significantly positively correlated with the decomposition rate (r = 0.783 and r = 0.375, P < 0.05). Based on 16S sequencing results, straw returning improved the microbial diversity of paddy soils by increasing unclassified bacteria and keeping dominant soil microorganism populations unchanged. The relative importance of individual microbial taxa was compared using random forest models. Proteobacteria, ammoniating bacteria, and potassium dissolving bacteria contributed to peroxidase activity. The significant contributors to phosphate monoesterase were Acidobacteriota, Desulfobacterota, ammoniating bacteria, cellulolytic bacteria, and potassium-dissolving bacteria. Proteobacteria, ammoniating bacteria, cellulolytic bacteria, and potassium-dissolving bacteria contributed to urease activity. Desulfobacterota, ammoniating bacteria, cellulolytic bacteria, and potassium-dissolving bacteria contributed to the neutral invertase activity. In conclusion, soil microbial community structure and function were affected within 2 years of straw returning, which was driven by the combined effects of soil organic carbon, available nitrogen, available potassium, and pH. With elapsing straw returning years, soil properties interacted with soil microbial communities, and a healthier soil micro-ecological environment would form.
- Description of Microbacterium luteum sp. nov., Microbacterium cremeum sp. nov., and Microbacterium atlanticum sp. nov., three novel C50 carotenoid producing bacteria
- Fuquan Xie , Siwen Niu , Xihuang Lin , Shengxiang Pei , Li Jiang , Yun Tian , Gaiyun Zhang
- J. Microbiol. 2021;59(10):886-897. Published online September 7, 2021
- DOI: https://doi.org/10.1007/s12275-021-1186-5
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- 14 Citations
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Abstract
- We have identified three Microbacterium strains, A18JL200T, NY27T, and WY121T, that produce C50 carotenoids. Taxonomy shows they represent three novel species. These strains shared < 98.5% 16S rRNA gene sequence identity with each other and were closely related to Microbacterium aquimaris JCM 15625T, Microbacterium yannicii JCM 18959T, Microbacterium ureisolvens CFH S00084T, and Microbacterium hibisci CCTCC AB 2016180T. Digital DNA-DNA hybridization (dDDH) values and average nucleotide identity (ANI) showed differences among the three strains and from their closest relatives, with values ranging from 20.4% to 34.6% and 75.5% to 87.6%, respectively. These values are below the threshold for species discrimination. Both morphology and physiology also differed from those of phylogenetically related Microbacterium species, supporting that they are indeed novel species. These strains produce C50 carotenoids (mainly decaprenoxanthin). Among the three novel species, A18JL200T had the highest total yield in carotenoids (6.1 mg/L or 1.2 mg/g dry cell weight). Unusual dual isoprenoid biosynthetic pathways (methylerythritol phosphate and mevalonate pathways) were annotated for strain A18JL200T. In summary, we found strains of the genus Microbacterium that are potential producers of C50 carotenoids, but their genome has to be investigated further.
- Gastrointestinal microbiota alteration induced by Mucor circinelloides in a murine model
- Katherine D. Mueller , Hao Zhang , Christian R. Serrano , R. Blake Billmyre , Eun Young Huh , Philipp Wiemann , Nancy P. Keller , Yufeng Wang , Joseph Heitman , Soo Chan Lee
- J. Microbiol. 2019;57(6):509-520. Published online May 27, 2019
- DOI: https://doi.org/10.1007/s12275-019-8682-x
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- 18 Citations
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Abstract
- Mucor circinelloides is a pathogenic fungus and etiologic agent of mucormycosis. In 2013, cases of gastrointestinal illness after yogurt consumption were reported to the US FDA, and the producer found that its products were contaminated with Mucor. A previous study found that the Mucor strain isolated from an open contaminated yogurt exhibited virulence in a murine systemic infection model and showed that this strain is capable of surviving passage through the gastrointestinal tract of mice. In this study, we isolated another Mucor strain from an unopened yogurt that is closely related but distinct from the first Mucor strain and subsequently examined if Mucor alters the gut microbiota in a murine host model. DNA extracted from a ten-day course of stool samples was used to analyze the microbiota in the gastrointestinal tracts of mice exposed via ingestion of Mucor spores. The bacterial 16S rRNA gene and fungal ITS1 sequences obtained were used to identify taxa of each kingdom. Linear regressions revealed that there are changes in bacterial and fungal abundance in the gastrointestinal tracts of mice which ingested Mucor. Furthermore, we found an increased abundance of the bacterial genus Bacteroides and a decreased abundance of the bacteria Akkermansia muciniphila in the gastrointestinal tracts of exposed mice. Measurements of abundances show shifts in relative levels of multiple bacterial and fungal taxa between mouse groups. These findings suggest that exposure of the gastrointestinal tract to Mucor can alter the microbiota and, more importantly, illustrate an interaction between the intestinal mycobiota and bacteriota. In addition, Mucor was able to induce increased permeability in epithelial cell monolayers in vitro, which might be indicative of unstable intestinal barriers. Understanding how the gut microbiota is shaped is important to understand the basis of potential methods of treatment for gastrointestinal illness. How the gut microbiota changes in response to exposure, even by pathogens not considered to be causative agents of food-borne illness, may be important to how commercial food producers prevent and respond to contamination of products aimed at the public. This study provides evidence that the fungal microbiota, though understudied, may play an important role in diseases of the human gut.
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