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  • 1
    Online Resource
    Online Resource
    Niche Modification by Sulfate-Reducing Bacteria Drives Microbial Community Assembly in Anoxic Marine Sediments
    American Society for Microbiology ; 2023
    In:  mBio Vol. 14, No. 2 ( 2023-04-25)
    Details
    In: mBio, American Society for Microbiology, Vol. 14, No. 2 ( 2023-04-25)
    Abstract: Sulfate-reducing bacteria (SRB) are essential functional microbial taxa for degrading organic matter (OM) in anoxic marine environments. However, there are little experimental data regarding how SRB regulates microbial communities. Here, we applied a top-down microbial community management approach by inhibiting SRB to elucidate their contributions to the microbial community during OM degradation. Based on the highly replicated microcosms ( n  = 20) of five different incubation stages, we found that many microbial community properties were influenced after inhibiting SRB, including the composition, structure, network, and community assembly processes. We also found a strong coexistence pattern between SRB and other abundant phylogenetic lineages via positive frequency-dependent selection. The relative abundances of the families Synergistaceae , Peptostreptococcaceae , Dethiosulfatibacteraceae , Prolixibacteraceae , Marinilabiliaceae , and Marinifilaceae were simultaneously suppressed after inhibiting SRB during OM degradation. A close association between SRB and the order Marinilabiliales among coexisting taxa was most prominent. They contributed to preserved modules during network successions, were keystone nodes mediating the networked community, and contributed to homogeneous ecological selection. The molybdate tolerance test of the isolated strains of Marinilabiliales showed that inhibited SRB (not the inhibitor of SRB itself) triggered a decrease in the relative abundance of Marinilabiliales . We also found that inhibiting SRB resulted in reduced pH, which is unsuitable for the growth of most Marinilabiliales strains, while the addition of pH buffer (HEPES) in SRB-inhibited treatment microcosms restored the pH and the relative abundances of these bacteria. These data supported that SRB could modify niches to affect species coexistence. IMPORTANCE Our model offers insight into the ecological properties of SRB and identifies a previously undocumented dimension of OM degradation. This targeted inhibition approach could provide a novel framework for illustrating how functional microbial taxa associate the composition and structure of the microbial community, molecular ecological network, and community assembly processes. These findings emphasize the importance of SRB during OM degradation. Our results proved the feasibility of the proposed study framework, inhibiting functional taxa at the community level, for illustrating when and to what extent functional taxa can contribute to ecosystem services.
    Type of Medium: Online Resource
    ISSN: 2150-7511
    URL: Article
    DOI: 10.1128/mbio.03535-22
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2023
    detail.hit.zdb_id: 2557172-2
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  • 2
    Online Resource
    Online Resource
    Table_1.xlsx
    Frontiers Media SA ; 2023
    In:  Frontiers in Marine Science Vol. 10 ( 2023-6-30)
    Details
    In: Frontiers in Marine Science, Frontiers Media SA, Vol. 10 ( 2023-6-30)
    Abstract: Biological nitrogen fixation plays a crucial role in the marine nitrogen cycle, impacting global marine productivity and related carbon fluxes. The strains were analyzed by gene annotation, growth conditions and phylogenetic analysis of 16S rRNA gene sequences.These two strains were isolated from the coastal sediment at Xiaoshi Island in Weihai, China. The strains were analyzed by gene annotation, growth conditions and phylogenetic analysis of 16S rRNA gene sequences. It was revealed that strains D04 T and AAT T contain a set of nif gene clusters responsible for nitrogen fixation. Cell are yellow-colored, Gram-stain-negative, facultatively anaerobic, and rod-shaped bacteria. The optimal growth conditions for strain D04 T were found to be at 33 °C, pH 7.0, and in 2% (w/v) NaCl, while strain AAT T prefers growth conditions at 33 °C, pH 6.5, and in 3% (w/v) NaCl. The highest similarity of strains D04 T and AAT T was to Saccharicrinis fermentans NBRC 15936 T , with a similarity of 94.1% and 94.8%, respectively. The 16S rRNA gene sequence similarity between the two strains was 96.6%. These novel strains were found to represent new taxa of the Marinilabiliaceae family, and we propose the names Plebeiobacterium marinum gen. nov., sp. nov. and Plebeiobacterium sediminum sp. nov. with type strains D04 T (MCCC 1H00493 T = KCTC 92026 T ) and AAT T (MCCC 1H00485 T = KCTC 92028 T ), respectively. In this study, nitrogen fixation genes were predicted for 53 strains from the whole order Marinilabiliales and it was found that nitrogen fixation gene clusters were present in 26 strains. These gene clusters were found in every family in the order, highlighting that the presence of nitrogen-fixing gene clusters in the order is common. Nitrogen-fixing bacteria in sediments play an important role in various biogeochemical cycles. Thus, understanding the oceanic nitrogen cycle can provide insights into the energy flow of marine systems.
    Type of Medium: Online Resource
    ISSN: 2296-7745
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.3389/fmars.2023.1213051
    DOI: 10.3389/fmars.2023.1213051.s001
    DOI: 10.3389/fmars.2023.1213051.s002
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2023
    detail.hit.zdb_id: 2757748-X
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  • 3
    Online Resource
    Online Resource
    Gaoshiqia sediminis gen. nov., sp. nov., isolated from coastal sediment
    Microbiology Society ; 2023
    In:  International Journal of Systematic and Evolutionary Microbiology Vol. 73, No. 5 ( 2023-05-01)
    Details
    In: International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, Vol. 73, No. 5 ( 2023-05-01)
    Abstract: A Gram-stain-negative, facultative anaerobic, motile, rod-shaped and orange bacterium, designated A06 T , was obtained off the coast of Weihai, PR China. Cells were 0.4–0.5×0.6–1.0 µm in size. Strain A06 T grew at 20–40 °C (optimum, 33 °C), at pH 6.0–8.0 (optimum, pH 6.5–7.0) and in the presence of 0–8 % NaCl (w/v) (optimum, 2 %). Cells were oxidase and catalase positive. Menaquinone-7 was detected as the major respiratory quinone. The dominant cellular fatty acids were identified as C 15:0 2-OH, iso-C 15:0 , anteiso-C 15:0 and iso-C 15:1  ω 6 c . The DNA G+C content of strain A06 T was 46.1 mol%. The polar lipids were phosphatidylethanolamine, one aminolipid, one glycolipid and three unidentified lipids. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain A06 T is a member of the family Prolixibacteraceae and exhibited the highest sequence similarity to Mangrovibacterium diazotrophicum DSM 27148 T (94.3 %). Based on its phylogenetic and phenotypic characteristics, strain A06 T is considered to represent a novel genus in the family Prolixibacteraceae , for which the name Gaoshiqia gen. nov. is proposed. The type species is Gaoshiqia sediminis sp. nov., with type strain A06 T (=KCTC 92029 T =MCCC 1H00491 T ). The identification and acquisition of microbial species and genes in sediments will help broaden the understanding of microbial resources and lay a foundation for its application in biotechnology. Strain A06 T uses an enrichment method, so the isolation of strain A06 T is of great significance to the enrichment of marine microbial resources.
    Type of Medium: Online Resource
    ISSN: 1466-5026 , 1466-5034
    URL: Article
    DOI: 10.1099/ijsem.0.005855
    Language: English
    Publisher: Microbiology Society
    Publication Date: 2023
    detail.hit.zdb_id: 215062-1
    detail.hit.zdb_id: 2056611-6
    SSG: 12
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