Marlow Jeffrey, Spietz Rachel, Kim Keun-Young, Ellisman Mark, Girguis Peter, Hatzenpichler Roland
Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave, Cambridge, Massachusetts, 02138, USA.
Department of Chemistry and Biochemistry, Department of Microbiology and Cell Biology, Thermal Biology Institute, and Center for Biofilm Engineering, Montana State University, Bozeman, Montana, 59717, USA.
Environ Microbiol. 2021 Aug;23(8):4756-4777. doi: 10.1111/1462-2920.15667. Epub 2021 Aug 4.
Coastal salt marshes are key sites of biogeochemical cycling and ideal systems in which to investigate the community structure of complex microbial communities. Here, we clarify structural-functional relationships among microorganisms and their mineralogical environment, revealing previously undescribed metabolic activity patterns and precise spatial arrangements within salt marsh sediment. Following 3.7-day in situ incubations with a non-canonical amino acid that was incorporated into new biomass, samples were resin-embedded and analysed by correlative fluorescence and electron microscopy to map the microscale arrangements of anabolically active and inactive organisms alongside mineral grains. Parallel sediment samples were examined by fluorescence-activated cell sorting and 16S rRNA gene sequencing to link anabolic activity to taxonomic identity. Both approaches demonstrated a rapid decline in the proportion of anabolically active cells with depth into salt marsh sediment, from ~60% in the top centimetre to 9.4%-22.4% between 2 and 10 cm. From the top to the bottom, the most prominent active community members shifted from sulfur cycling phototrophic consortia, to putative sulfate-reducing bacteria likely oxidizing organic compounds, to fermentative lineages. Correlative microscopy revealed more abundant (and more anabolically active) organisms around non-quartz minerals including rutile, orthoclase and plagioclase. Microbe-mineral relationships appear to be dynamic and context-dependent arbiters of biogeochemical cycling.
沿海盐沼是生物地球化学循环的关键场所，也是研究复杂微生物群落结构的理想系统。在此，我们阐明了微生物与其矿物学环境之间的结构 - 功能关系，揭示了盐沼沉积物中先前未描述的代谢活动模式和精确的空间排列。在用一种掺入新生物质的非标准氨基酸进行3.7天原位培养后，将样品用树脂包埋，并通过相关荧光和电子显微镜分析，以绘制合成代谢活跃和不活跃生物体与矿物颗粒的微观排列图。通过荧光激活细胞分选和16S rRNA基因测序对平行沉积物样品进行检测，以将合成代谢活性与分类身份联系起来。两种方法均表明，随着盐沼沉积物深度的增加，合成代谢活跃细胞的比例迅速下降，从顶部1厘米处的约60%降至2至10厘米之间的9.4% - 22.4%。从顶部到底部，最突出的活跃群落成员从硫循环光合共生体，转变为可能氧化有机化合物的假定硫酸盐还原细菌，再转变为发酵谱系。相关显微镜显示，在包括金红石、正长石和斜长石在内的非石英矿物周围存在更丰富（且合成代谢更活跃）的生物体。微生物与矿物的关系似乎是生物地球化学循环的动态且依赖于环境的仲裁者。
