Brown Jennifer L, Swift Candice L, Mondo Stephen J, Seppala Susanna, Salamov Asaf, Singan Vasanth, Henrissat Bernard, Drula Elodie, Henske John K, Lee Samantha, LaButti Kurt, He Guifen, Yan Mi, Barry Kerrie, Grigoriev Igor V, O'Malley Michelle A
Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.
US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Biotechnol Biofuels. 2021 Dec 10;14(1):234. doi: 10.1186/s13068-021-02083-w.
Anaerobic fungi and methanogenic archaea are two classes of microorganisms found in the rumen microbiome that metabolically interact during lignocellulose breakdown. Here, stable synthetic co-cultures of the anaerobic fungus Caecomyces churrovis and the methanogen Methanobacterium bryantii (not native to the rumen) were formed, demonstrating that microbes from different environments can be paired based on metabolic ties. Transcriptional and metabolic changes induced by methanogen co-culture were evaluated in C. churrovis across a variety of substrates to identify mechanisms that impact biomass breakdown and sugar uptake. A high-quality genome of C. churrovis was obtained and annotated, which is the first sequenced genome of a non-rhizoid-forming anaerobic fungus. C. churrovis possess an abundance of CAZymes and carbohydrate binding modules and, in agreement with previous studies of early-diverging fungal lineages, N6-methyldeoxyadenine (6mA) was associated with transcriptionally active genes. Co-culture with the methanogen increased overall transcription of CAZymes, carbohydrate binding modules, and dockerin domains in co-cultures grown on both lignocellulose and cellulose and caused upregulation of genes coding associated enzymatic machinery including carbohydrate binding modules in family 18 and dockerin domains across multiple growth substrates relative to C. churrovis monoculture. Two other fungal strains grown on a reed canary grass substrate in co-culture with the same methanogen also exhibited high log2-fold change values for upregulation of genes encoding carbohydrate binding modules in families 1 and 18. Transcriptional upregulation indicated that co-culture of the C. churrovis strain with a methanogen may enhance pyruvate formate lyase (PFL) function for growth on xylan and fructose and production of bottleneck enzymes in sugar utilization pathways, further supporting the hypothesis that co-culture with a methanogen may enhance certain fungal metabolic functions. Upregulation of CBM18 may play a role in fungal-methanogen physical associations and fungal cell wall development and remodeling.
厌氧真菌和产甲烷古菌是瘤胃微生物群中发现的两类微生物，它们在木质纤维素分解过程中发生代谢相互作用。在此，构建了厌氧真菌曲形盲肠菌（Caecomyces churrovis）和产甲烷菌布氏甲烷杆菌（Methanobacterium bryantii，非瘤胃原生菌）的稳定合成共培养物，证明来自不同环境的微生物可以基于代谢联系进行配对。在多种底物上评估了产甲烷菌共培养物诱导的曲形盲肠菌的转录和代谢变化，以确定影响生物质分解和糖摄取的机制。获得并注释了曲形盲肠菌的高质量基因组，这是首个测序的非形成根状菌的厌氧真菌基因组。曲形盲肠菌拥有丰富的碳水化合物活性酶（CAZyme）和碳水化合物结合模块，并且与先前对早期分化真菌谱系的研究一致，N6-甲基脱氧腺嘌呤（6mA）与转录活性基因相关。与产甲烷菌共培养增加了在木质纤维素和纤维素上生长时共培养物中CAZyme、碳水化合物结合模块和锚定蛋白结构域的整体转录，并导致相对于曲形盲肠菌单培养物，在多种生长底物上编码相关酶机制（包括第18家族的碳水化合物结合模块和锚定蛋白结构域）的基因上调。在与同一产甲烷菌共培养的芦苇雀麦草底物上生长的另外两种真菌菌株，在编码第1和18家族碳水化合物结合模块的基因上调方面也表现出高的log2倍变化值。转录上调表明曲形盲肠菌菌株与产甲烷菌共培养可能增强丙酮酸甲酸裂解酶（PFL）在木聚糖和果糖上生长以及糖利用途径中瓶颈酶产生的功能，进一步支持了与产甲烷菌共培养可能增强某些真菌代谢功能的假设。CBM18的上调可能在真菌-产甲烷菌物理关联以及真菌细胞壁发育和重塑中起作用。
