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| 1 | Microbial dark matter coming to light:challenges and opportunities显示文摘Microbes are the most abundant and diverse cellular life forms on Earth and colonize a wide range of environmental niches.However,more than 99%of bacterial and archaeal species have not been obtained in pure culture[1]and we have only glimpsed the surface of this mysterious microbial world. | Jian-Yu Jiao Lan Liu Zheng-Shuang Hua Bao-Zhu Fang En-Min Zhou Nimaichand Salam Brian PHedlund Wen-Jun Li | 2021 | National Science Review2021，8，3： | 6 |
| 2 | Endophytic bacteria associated with endangered plant Ferula sinkiangensis K. M. Shen in an arid land: diversity and plant growth-promoting traits显示文摘Ferula spp. are traditional medicinal plants found in arid land. Large-scale excavation for extracting bioactive compounds from the plants in arid regions of Xinjiang over the last few years has, however, significantly decreased their distributions. Due to the urgent need for preservation of these plant resources, along with the need of searching for alternative source of the useful metabolites, it is important to screen the endophytic microbial resources associated with the plant Ferula sinkiangensis K. M. Shen. In the study, a total of 125 endophytic bacteria belonging to 3 phyla, 13 orders, 23 families, and 29 genera were isolated based on 16 SrRNA gene sequencing data. Among the different isolates, three strains isolated from roots were potential novel species of the genera Por phyrobacter, Paracoccus and Amycolatopsis. In this study, 79.4% and 57.1% of the total isolates were capable of producing indole-3-acetic acid(IAA) and siderophore, respectively. And, 40.6% of the strains inhibit the growth of fungal pathogen Alternaria alternata, 17.2% and 20.2% strains were positive for antagonism against Verticillium dahlia 991 and V. dahlia 7, respectively. These results demonstrated that F. sinkiangensis is a rich reservoir of endophytic bacterial resources with potential for production of biologically important functions such as plant growth-promoting factors. | LIU Yonghong GUO Jianwei LI Li Mipeshwaree D ASEM ZHANG Yongguang Osama A MOHAMAD Nimaichand SALAM LI Wenjun | 2017 | Journal of Arid Land2017，9，3： | 6 |
| 3 | From ecophysiology to cultivation methodology:filling the knowledge gap between uncultured and cultured microbes显示文摘Earth is dominated by a myriad of microbial communities,but the majority fails to grow under in situ laboratory conditions.The basic cause of unculturability is that bacteria dominantly occur as biofilms in natural environments.Earlier improvements in the culture techniques are mostly done by optimizing media components.However,with technological advancement particularly in the field of genome sequencing and cell imagining techniques,new tools have become available to understand the ecophysiology of microbial communities.Hence,it becomes easier to mimic environmental conditions in the culture plate.Other methods include co-culturing,emendation of growth factors,and cultivation after physical cell sorting.Most recently,techniques have been proposed for bacterial cultivation by employing genomic data to understand either microbial interactions(network-directed targeted bacterial isolation)or ecosystem engineering(reverse genomics).Hopefully,these techniques may be applied to almost all environmental samples,and help fill the gaps between the cultured and uncultured microbial communities. | Nimaichand Salam Wen-Dong Xian Mipeshwaree Devi Asem Min Xiao Wen-Jun Li | 2021 | Marine Life Science & Technology2021，3，2： | 4 |
| 4 | Comparative genomic analysis of Thermus provides insights into the evolutionary history of an incomplete denitrification pathway显示文摘Biological denitrification is a crucial process in the nitrogen biogeochemical cycle,and Thermus has been reported to be a significant heterotrophic denitrifier in terrestrial geothermal environments.However,neither the denitrification potential nor the evolutionary history of denitrification genes in the genus Thermus or phylum Deinococcota is well understood.Here,we performed a comparative analysis of 23 Thermus genomes and identified denitrification genes in 15 Thermus strains.We confirmed that Thermus harbors an incomplete denitrification pathway as none of the strains contain the nosZ gene.Ancestral character state reconstructions and phylogenetic analyses showed that narG,nirS,and norB genes were acquired by the last common ancestor of Thermales and were inherited vertically.In contrast,nirK of Thermales was acquired via two distinct horizontal gene transfers from Proteobacteria to the genus Caldithermus and from an unknown donor to the common ancestor of all known Thermus species except Thermus filiformis.This study expands our understanding of the genomic potential for incomplete denitrification in Thermus,revealing a largely vertical evolutionary history of the denitrification pathway in the Thermaceae,and supporting the important role for Thermus as an important heterotrophic denitrifier in geothermal environments. | Jian-Yu Jiao Zheng-Han Lian Meng-Meng Li Nimaichand Salam En-Min Zhou Lan Liu Hong Ming Guoxing Nie Wensheng Shu Guoping Zhao Brian P.Hedlund Wen-Jun Li | 2022 | mLife2022，1，2： | 1 |
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