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? ? ? ?土壤有機質 (SOM) 是地球上最大的陸地有機碳庫，SOM 動態對全球碳循環有重大影響。SOM 對土地管理和氣候變化敏感，而SOM 庫顯著影響土壤健康、農業生產力和氣候穩定性。然而，關于 SOM持久性和損失的機制仍然不確定。微生物是 SOM 分解、穩定和礦化的主要驅動因素，土壤微生物在控制全球 C 通量方面發揮著關鍵作用，但決定 SOM 動態的微生物機制仍不清楚。
? ? ??2021年11月23日，權威綜合學術期刊PNAS刊發相關研究論文，康奈爾大學Daniel H. Buckley為論文通訊作者，博士生Samuel E. Barnett為論文第一作者，論文題目：Multisubstrate DNA stable isotope probing reveals guild structure of bacteria that mediate soil carbon cycling。
? ? ??作者采用了多底物、DNA 穩定同位素探測實驗示蹤不同生物可利用度、不同來源碳的細菌同化過程。這種方法使我們能夠通過測量不同微生物相互作用的碳同化動力學來測量微生物對 SOM的貢獻。作者鑒定了 1,286 個細菌類群，它們在 48 天的時間里同化了農業土壤中的 13C。細菌類群的整體 13C 同化動力學受13C的來源和時間影響，表現出低系統發育保守性。因此確定了由具有相似 13C 同化動力學的分類群組成結構。碳源生物利用度解釋了碳礦化動態和群落結構的顯著變化，并且細菌生長動態因碳添加而顯著不同。微生物結構解釋了大陸和全球范圍內細菌生物地理分布的變化。因此，可見，了解原位生長動態對于了解微生物對土壤碳循環的貢獻至關重要。
圖1. 實驗設計和流程
? ? ? This experiment employed soil microcosms, each amended with all nine C sources (added at 0.4 mg C per gram of soil), only one of which was >99% 13C-labeled in treatment microcosms. Control microcosms had all nine C sources added but none were isotopically labeled. Microcosms were destructively sampled at multiple time points (black bars) based on mineralization rates from preliminary experiment. Headspace samples were taken every 1 to 7 d. DNA extracted from microcosm soil was used both for DNA-SIP and whole bacterial community sequencing (unfractionated).
圖2. C 源礦化動態
? ? ? C source mineralization dynamics varied based on bioavailability. (A) 13C mineralization rates and (B) cumulative amounts of 13C mineralized per gram dry weight of soil. (A, Inset) A finer-scale representation of the 13C mineralization rates over days 0 to 10. Error bars represent ± SD among microcosm replicates (n = 3).
圖3. 1,286 個 OTU 顯著差異的 13C 標記特征
? ? ? The dynamics of C assimilation varied across the 1,286 OTUs that exhibited significant 13C labeling. OTUs are ordered by their phylogeny with phylum, or class for Proteobacteria, indicated by different colors in the phylogenetic tree. Only phyla/classes with 10 or more 13C-labeled OTUs are colored, with others colored gray. Each vertical block indicates 13C-labeling results for a single day as specified at the top. Each column within a block indicates results for a given substrate as specified along the bottom. Rows display 13C-labeling dynamics for each OTU as follows: red bars indicate 13C-labeling, light gray bars indicate OTU detection in the gradient but no evidence of labeling, white indicates the OTU was not detected in the gradient. Phylum/class abbreviations: Bact. = Bacteroidetes, Acido. = Acidobacteria, Gemm. = Gemmatimonadetes, Chl-flx. = Chloroflexi, Firmi. = Firmicutes, Actino. = Actinobacteria, Verruc. = Verrucomicrobia, Plancto. = Planctomycetes, Beta. = Betaproteobacteria, Gamma. = Gammaproteobacteria, Delta. = Deltaproteobacteria, Alpha. = Alphaproteobacteria.
圖4. 代表公會 2 (OTU.197)、14 (OTU.22) 和 19 (OTU.7163) 最豐富的 OTU 的生長和 13C 標記動態
? ? ? Growth and 13C-labeling dynamics of the most abundant OTUs representing guilds 2 (OTU.197), 14 (OTU.22), and 19 (OTU.7163), which are the guilds most differentiated by PCA (Fig. 5E). (A) The 13C-labeling pattern differs between the three exemplar OTUs. Circles show times when 13C labeling was detected for each substrate and OTU responses are identified by circle color as defined in B. Black rectangles indicate the times when DNA-SIP was performed for each 13C-labeled substrate and red rectangles indicate the time of peak C mineralization for each C source (Fig. 2). (B) Growth dynamics differ between the three exemplar OTUs. Normalized abundance (expressed as micrograms of DNA) is calculated from relative abundance values normalized by rrn copy number and DNA yield.
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