2023, Vol. 63
表1(Table 1)
我国产甲烷古菌研究进展与展望
http://dx.doi.org/10.13343/j.cnki.wsxb.20230104
中国科学院微生物研究所，中国微生物学会
中国科学院微生物研究所，中国微生物学会
文章信息
- 易悦, 周卓, 黄艳, 承磊. 2023
- YI Yue, ZHOU Zhuo, HUANG Yan, CHENG Lei.
- 我国产甲烷古菌研究进展与展望
- Methanogen research in China: current status and prospective
- 微生物学报, 63(5): 1796-1814
- Acta Microbiologica Sinica, 63(5): 1796-1814
-
文章历史
- 收稿日期：2023-02-23
- 网络出版日期：2023-04-24
引用本文 |
易悦, 周卓, 黄艳, 承磊. 我国产甲烷古菌研究进展与展望[J]. 微生物学报, 2023, 63(5): 1796-1814.
Yi Yue, Zhou Zhuo, Huang Yan, Cheng Lei. Methanogen research in China: current status and prospective[J]. Acta Microbiologica Sinica, 2023, 63(5): 1796-1814.
我国产甲烷古菌研究进展与展望
1. 农业农村部成都沼气科学研究所 农业农村部农村可再生能源开发利用重点实验室, 四川 成都 610041;
2. 中国厌氧微生物菌种保藏管理中心, 四川 成都 610041
2. 中国厌氧微生物菌种保藏管理中心, 四川 成都 610041
摘要：产甲烷古菌广泛分布在湿地、水稻田、动物瘤胃、油藏、海洋和热液等缺氧环境，在全球碳素循环、气候变化和清洁能源生产等领域发挥着重要作用，一直是国内外的研究热点。本文简要回顾了我国产甲烷古菌的研究进展，重点阐述了产甲烷古菌的资源与分类、生理生化、分子生物学、生态学功能和应用等方面的研究进展，并展望了产甲烷古菌的未来研究趋势。
关键词：产甲烷古菌 生物学功能 碳循环
Methanogen research in China: current status and prospective
1. Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture and Rural Affairs, Chengdu Biogas Institute, Ministry of Agriculture and Rural Affairs, Chengdu 610041, Sichuan, China;
2. China Collection of Anaerobic Microorganisms, Chengdu 610041, Sichuan, China
2. China Collection of Anaerobic Microorganisms, Chengdu 610041, Sichuan, China
Abstract: Methanogens are widely distributed in anaerobic environments, such as wetlands, paddy fields, animal rumens, oil reservoirs, oceans, and hydrothermal vents. They play critical roles in global carbon cycling, climate change, and clean energy production, making them a hot research topic both domestically and internationally. This article briefly reviews the research progress of methanogens in China, focusing on their resources and taxonomy, physiology and biochemistry, molecular biology, ecological roles, and applications. The future research trends of methanogens are also highlighted.
Keywords:
methanogen biological function carbon cycle
产甲烷古菌被认为是地球上最早的生命形式之一，是研究生命起源与进化的重要模式物种[1]。全球每年约有一半以上的CH4是由产甲烷古菌在缺氧环境中形成的[2]。另一方面，CH4是主要的温室气体之一，在20年尺度范围内，CH4的增温效应是CO2的84倍[3]。因此，产甲烷古菌对全球气候变化也有重要影响。同时，产甲烷古菌产生的CH4可以替代化石能源、补充能源供给、减少化石燃料的使用和减轻环境污染[4]。因此深入理解产甲烷古菌的微生物学机制和生态学功能，有助于认识生命进化过程、揭示碳循环机制，并指导开发绿色可再生能源。
1 资源与分类产甲烷古菌对氧气敏感、培养条件苛刻，分离培养难度较大。1933年，Stephenson等从英国乌斯河的污泥中分离出第一株利用甲酸产甲烷的产甲烷古菌纯培养物[5]。1980年，我国学者周孟津等从猪粪发酵液中分离获得甲烷八叠球菌(Methanosarcina)的纯培养物，它具有代谢甲醇、甲胺、乙酸盐和H2/CO2产甲烷的能力，实现了我国产甲烷古菌分离培养的突破[6]。随后，我国学者先后从沼气池、反应器、湿地、水稻土等环境中分离出多株产甲烷古菌(附表 1，数据已提交至国家微生物科学数据中心，编号为NMDCX0000196)，但是一直没有新物种的报道。直到2005年，东秀珠团队才从厌氧消化器中分离鉴定出第一个新种Methanobacterium beijingense sp. nov. (表 1)[7]。2007年，本团队从胜利油田分离鉴定了甲基营养型产甲烷古菌新属(Methermicoccus shengliensis gen. nov., sp. nov.)，并提出新科Methermicoccaceae fam. nov.，实现了我国在产甲烷古菌资源分类从新种到新科的跨越[8]。截至2022年11月，有效发表的产甲烷古菌共有171个种，分属于38属、17科和8目中。其中我国科学家共提出1个新科、1个新属和14个新种(表 1)[7-19]。
表 1. 我国学者分离鉴定的产甲烷古菌新物种
Table 1. Novel methanogenic taxon isolated and identified by Chinese scholars
| Isolate species | Substrate | Morphology (μm) | Optimal growth conditions | Growth factor | Source | Genome | 16S rRNA | Reference | |
| pH | T/℃ | ||||||||
| Methanobacterium beijingense 8-2T | H2/CO2, formate | Rod, 0.4–0.5×3–5 | 7.2 | 37 | Nd | Anaerobic digesters | Nd | AY350742 | [7] |
| Methanobacterium flexile GHT | H2/CO2, formate | Rod, 0.3–0.5×2–5 | 7.0–7.5 | 35–38 | YE | Gahai lake | Nd | EU333914 | [9] |
| Methanobacterium movens TS-2T | H2/CO2 | Rod, 0.3–0.5×2–5 | 7.2–7.5 | 35–38 | YE | Tuosu lake | Nd | EU366499 | [9] |
| Methanocella conradii HZ254T | H2/CO2 | Rod, 0.2–0.3×1.4–2.8 | 6.8 | 55 | Nd | Rice field soil located in Hangzhou | GCA_000251105.1 | CP003243 | [10] |
| Methanococcoides orientis LMO-1T | Methanol, methylamine, dimethylamine and trimethylamine | Irregular cocci, 1.0–2.0 | 7.0–7.5 | 30–35 | Nd | East China Sea sediment | GCA_021184045.1 | NR_177426.1 | [11] |
| Methanoculleus hydrogenitrophicus HCT | H2/CO2 | Irregular cocci, 0.8–2.0 | 6.6 | 37 | Nd | Zoige wetland | Nd | FJ977567 | [12] |
| Methanoculleus receptaculi ZC-2T | H2/CO2, formate | Cocci, 0.8–1.7 | 7.5–7.8 | 50–55 | Nd | Shengli oilfield | Nd | DQ787476 | [13] |
| Methanoculleus sediminis S3FaT | H2/CO2, formate | Cocci, 0.5–1.0 | 7.1 | 37 | Nd | Mud volcano | GCA_001017125.1 | JXOJ01000002 | [14] |
| Methanofollis fontis FWC-SCC2T | H2/CO2, formate | Cocci, 0.8–1.2 | 6.7–7.0 | 37 | Nd | Deep-sea sediments | GCA_004297185.1 | MG437305 | [15] |
| Methanolobus halotolerans SY-01T | Methanol | Cocci, 0.8–1.0 | 8.0 | 30 | YE | Sediment of saline Lake Tus | GCA_004745425.1 | MG437307 | [16] |
| Methanosaeta harundinacea 8AcT | Acetate | Rod, 0.8–1.0×3–5 | 7.2–7.6 | 34–37 | YE, Trp | Anaerobic sludge blanket reactor | GCA_000235565.1 | AY817738 | [17] |
| Methanospirillum psychrodurum X-18T | H2/CO2 | Rod, 0.4–0.5×11–62 | 7.0 | 25 | YE | Soil of the Madoi wetland | Nd | KF153052 | [18] |
| Methanothermobacter crinale Tm2T | H2/CO2 | Slightly curved rods, 0.3–0.5×2.2–5.9 | 6.9 | 65 | Nd | Production water of oil reservoirs | Nd | HQ283273 | [19] |
| Methermicoccus shengliensis ZC-1T | Methanol, methylamine and trimethylamine | Cocci, 0.7–1.0 | 6.0–6.5 | 65 | SF, CoM | Oil-production water | GCA_000711905.1 | JONQ01000007 | [8] |
| YE: Yeast extract; Trp: Tryptone; SF: Sludge fluids; CoM: Coenzyme M; Nd: Not report. | |||||||||
过去认为产甲烷古菌仅分布在古菌域的广古菌门(Euryarchaeota)。2015年，国外学者利用宏基因组技术，发现Candidatus Bathyarchaeota类群中BA1和BA2具有利用H2还原甲基化合物产甲烷的代谢潜力[20]，首次提出产甲烷古菌可能也分布在广古菌门以外的分支上。截至目前，国内外多项研究从Ca. Bathyarchaeota、Ca. Korarchaeota、Ca. Nezhaarchaeota、Thermoproteota、Ca. Thermoplasmatota和Ca. Verstraetearchaeota等类群中发现25个未培养产甲烷古菌新物种(新属及以上分类单元) (表 2)[20-30]。其中我国科学家作为主要贡献者，参与了11个新属的提出，包括Ca. Nezhaarchaeota这个新门。本团队首次通过培养实验，证明了Ca. Verstraetearchaeota古菌具有氢依赖的甲醇和甲氨还原产甲烷能力(预印版https://doi.org/10.21203/rs.3.rs-2501667/v1)。
表 2. 新型潜在产甲烷古菌
Table 2. Novel candidate methanogenic archaea
| Phylum | Genus | Metabolic type | Source | Research group | Reference |
| Ca. Bathyarchaeotaa | BA1 and BA2 | MM | Coal-bed methane | TYSON GW | [20] |
| Euryarchaeota | Ca. Methanohalarchaeum | MM | Salt lake | KOONIN EV | [31] |
| Ca. Methanofastidiosum | MM | Anaerobic digestion reactor | LIU WT | [32] | |
| Ca. Methanoliparum | ALM | Petroleum sample | LI WJc | [33] | |
| Ca. Methanolliviera | ALM | Oil seeps | LI WJc | [33] | |
| Ca. Methanoflorens | HM | Rice, wetland, sediment, permafrost | TYSON GW | [34] | |
| Ca. Methanomixotrophus | MM | Oil reservoir | MU BZc | [35] | |
| Ca. Geoarchaeotab | Cren_UShs and Cren_JZhs | HM & AM | Hot spring | ZHANG Tc | [21] |
| Ca. Korarchaeotaa | Ca. Methanodesulfokores | MM | Hot spring | MCKAY LJ | [22] |
| Ca. Nezhaarchaeotab | WYZ-LMO7 and WYZ-LMO8 | HM | Hot spring | WANG FP and XIAO Xc | [23] |
| Ca. Thermoplasmatota | Ca. Methanomethylophilus | MM | Gut | BRUGÈRE JF | [24] |
| Ca. Methanoplasma | MM | Gut | BRUNEA A | [25] | |
| Ca. Methanogranum | MM | Anaerobic sludge | IINO T | [26] | |
| Ca. Methanospyradousia | MM | Gut | HILDEBRAND F | [27] | |
| Thermoproteota | Ca. Methylarchaeum | MM | Hot spring | HOU LJc | [28] |
| Ca. Methanotowutia | MM | Lake | HOU LJc | [28] | |
| Ca. Methanoinsularis | MM | Harbour | HOU LJc | [28] | |
| Ca. Methanoporticola | MM | Harbour | HOU LJc | [28] | |
| Ca. Verstraetearchaeotaa | Ca. Methanomethylicus | MM | Anaerobic digestion reactor | TYSON GW | [29] |
| Ca. Methanosuratincola | MM | Coalbed methane well | TYSON GW | [29] | |
| Ca. Methanohydrogenicus | HM | Yellowstone national park | QUAKE SR | [30] | |
| Ca. Methanomedium | HM | Yellowstone national park | QUAKE SR | [30] | |
| a: Recently GTDB has reclassified it as a subordinate class of Thermoproteota; b: GTDB has recently reclassified it as an order of Thermoproteota; c: Chinese. AM: Acetoclastic methanogensis; HM: Hydrogentrophic methanogensis; MM: Methylotrophic methanogensis; ALM: Alkylotrophic methanogensis. | |||||
2 产甲烷途径
产甲烷古菌底物谱简单，一般认为其只能利用少数的C1和C2化合物生长。根据底物谱，产甲烷古菌的产甲烷途径可分为CO2还原途径(hydrogenotrophic)、乙酸发酵途径(acetoclastic)和甲基裂解途径(methylotrophic)[36-37]。进行CO2还原途径的产甲烷古菌可以利用H2作为电子供体将CO2还原为CH4；而采用乙酸发酵途径的产甲烷古菌可以将乙酸分解成CH4和CO2；甲基裂解途径的产甲烷古菌可以将简单的甲基类化合物降解产生CH4和CO2，还有一类特殊的甲基营养型产甲烷古菌需要H2提供电子还原甲基类物质产甲烷[38]。Methanosarcina是目前已被证实唯一可以同时利用CO2、乙酸和简单甲基类化合物产甲烷的古菌。而一直认为仅能利用乙酸产甲烷的Methanosaeta (Methanothrix)，被发现可以利用种间直接电子传递获得的电子还原CO2产甲烷[39]。2016年，日本科学家发现M. shengliensis具有直接降解煤炭中的甲氧基化合物产甲烷的功能，提出了第4条产甲烷途径——甲氧基营养型产甲烷途径(methoxylotrophic)[40]。2022年，本团队联合深圳大学李猛和德国马普海洋所Gunter Wegener等团队，通过稳定碳同位素示踪培养、宏基因组和宏转录组测序及高分辨质谱分析，证实了一种新型的产甲烷古菌Ca. Methanoliparum能够直接降解C13及以上正构烷烃、C19及以上长链烷基环己烷和烷基苯产甲烷，提出并证实了第5条产甲烷途径——烷基型产甲烷途径(alkylotrophic)[41]。
3 分子生物学研究目前国外构建的产甲烷古菌的遗传操作系统有Methanococcus、Methanosarcina和Methanothermobacter属的古菌[42-46]。2022年，我国东秀珠团队在国外研究的基础上开发了Methanococcus maripaludis的CRISPR-Cas9基因操作体系，实现了对产甲烷古菌的靶向基因编辑[47]。东秀珠团队在产甲烷古菌分子机制方面也开展了大量研究，他们在Methanolobus psychrophilus R15中发现了mRNA的加工现象，打破了原核生物“mRNA不加工”的传统认知[48]。mRNA加工在产甲烷古菌适应低温环境时起着重要作用，拥有更长mRNA的甲醇甲基转移酶和乙酸激酶具有更好的低温稳定性[49-50]。同时他们阐明了M. psychrophilus中rRNA操纵子(16S-tRNAAla-23S-tRNACys-5S)是如何加工成熟的，完善了对古菌中rRNA成熟过程的认知[51]；发现了古菌第一个冷休克蛋白TRAM通过RNA伴侣作用，在基因组水平上调控基因表达，从而保证菌株在低温胁迫下能正常转录和生长[52-53]；发现了古生菌中第一个通用转录终止因子——保守核糖核酸酶aCPSF1，并阐明了终止机制，提出aCPSF1蛋白可以作为新的系统发育分子标志物，用于古菌的分类研究[54-55]。最新的研究结果表明，产甲烷古菌依赖aCPSF1转录终止模式与真核生物RNA聚合酶II终止机制相似，为“古菌是真核生物的进化起源”提供了新的证据[56]。此外，我国科学家在产甲烷古菌的膜脂研究中也作出了贡献，2022年，曾芝瑞团队通过在M. maripaludis中异源表达GDGT合成基因，首次鉴定出产甲烷古菌中参与GDGT生物合成的关键蛋白——四醚合成酶(tetraether synthase, Tes)[57]。2023年，司同团队通过在酿酒酵母(Saccharomyces cerevisiae)中异源表达来自Methanosarcina acetivorans的合成膜脂关键基因G1PDH (glycerol-1-phosphate dehydrogenase)、GGGPS (geranylgeranyl pyrophosphate synthase)和DGGGPS [(S)-2, 3-diO-geranylgeranylglyceryl phosphate synthase]，成功合成了具备古菌醚键特征的极性脂，首次在真核模式生物中实现了古菌特征细胞膜脂的异源合成[58]。以上研究填补了产甲烷古菌膜脂合成研究领域的空白，为认识和研究产甲烷古菌的膜脂合成奠定了基础。
4 生态分布 4.1 湿地湿地甲烷是大气中甲烷的主要来源，约占总排放的30%–50%[59]，产甲烷古菌是湿地甲烷排放的主要贡献者。青藏高原湿地和红树林湿地是我国湿地甲烷研究的主要对象，不同地区湿地中产甲烷古菌类型存在差异。青藏高原若尔盖高寒湿地以乙酸发酵产甲烷途径为主，伴随着CO2还原途径[60]。另有研究显示，甲基营养型产甲烷古菌对若尔盖湿地产甲烷的贡献同样不容忽视[61]。在西藏高海拔湿地土壤中，氢营养型产甲烷古菌则成为主要类群[62]。与青藏高原湿地不同，红树林湿地中SO42─含量较高，存在大量硫酸盐还原菌，它们对乙酸的亲和力远高于乙酸营养型产甲烷古菌[63]。因此在红树林湿地以氢营养型和甲基营养型产甲烷古菌为主，但不同地区的产甲烷古菌类群有一定差异。例如：在深圳福田红树林生态系统中，氢营养型和甲基营养型的产甲烷途径是主要的产甲烷代谢方式[64]。而在海南东寨港红树林沉积物中，氢营养型产甲烷古菌为主要的产甲烷菌类群[65-66]。温度、盐度、地理位置、有机碳浓度、导电碳材料和周围植被类型等均会影响产甲烷古菌群落结构。在10–30 ℃条件下，乙酸营养型产甲烷古菌占主导，而在45 ℃条件下，氢营养型产甲烷古菌占主导地位[67]。氢营养型产甲烷古菌在盐湖、水底沉积物和高浓度有机碳环境中占优势[68-70]，非盐湖、湿地浅层土和低浓度有机碳环境中乙酸营养型产甲烷古菌占优势[68-70]。导电碳材料促进了乙酸发酵产甲烷过程[71]。在刚毛荸荠土壤中甲基营养型产甲烷途径为主要贡献者，木里苔草土壤中乙酸产甲烷代谢途径占优势[72]。毛果草沼泽主要以氢营养型产甲烷菌为主，而黄叶草沼泽以氢营养型和乙酸营养型产甲烷菌为主[73]，这与植物细胞壁降解成不同的产甲烷前体物质有关[74]。尽管产甲烷古菌是湿地甲烷的主要贡献者，但湿地产甲烷潜力与产甲烷古菌数量无显著相关性[70]。有机碳浓度、降水和温度等是影响湿地甲烷排放量的重要因素，研究表明湿地产甲烷潜力主要由其中的溶解有机碳浓度决定[70]，降水导致的湿地扩张加剧了甲烷排放[75]，全球气温每升高1.5–2 ℃，湿地100年全球变暖潜力上升57%[76]。越来越多的研究表明，湿地甲烷排放正在加剧[76-77]，对全球碳排放控制目标构成威胁。现有湿地产甲烷相关研究为制定节能减排目标提供了科学依据。
4.2 水稻田水稻田也是大气甲烷的重要排放源，据颜晓元团队在2009年的报道，全球稻田CH4排放量约为25.6 Tg/a，占全球甲烷排放量的10%–25%[78]。国内关于水稻土中产甲烷古菌的研究最早可以追溯到1993年，钱泽澍团队采用改进的Hungate厌氧技术，结合稀释培养计数法(the most probable number, MPN)和滚管法测定了沉水水稻土中产甲烷古菌的数量，表明产甲烷古菌在根表生存而非在植物根内[79]。随着测序技术的发展，国内外多个研究发现产甲烷古菌未培养类群rice cluster I (RC-I)在水稻田中广泛存在[80-85]。陆雅海团队利用稳定同位素探针技术(stable isotope probe, SIP)证实RC-I在水稻根际甲烷形成过程中起关键作用[86]。同时他们发现RC-I在水稻田中具有抗氧胁迫的优势[87-88]。2012年，他们分离报道了RC-I类群的第3个新种Methanocella conradii sp. nov..[10]。
环境因子会影响产甲烷古菌群落的结构和活性，间接影响甲烷排放。陆雅海团队在这一方面做了大量研究，他们发现采用间歇性排水模式可以显著降低了产甲烷古菌活性，减少甲烷的产生[85]。排水间隔时间的长短也会影响CH4排放量，与长循环排水模式相比，在短循环模式下CH4排放显著降低[89]。不同的温度、水稻品种和植物残体也会影响甲烷产量。温度从15 ℃升高到45 ℃；CH4的产量增加[90]；杂交稻根际可溶性CH4浓度显著低于籼稻和粳稻[91]，而秸秆残渣比根残渣产生更多的CH4[90]。在水稻土中添加生物炭也会影响甲烷的生成，且不同来源的生物炭对生成甲烷的影响有差异。历红波团队发现来自稻草的生物炭促进了细菌与铁矿物之间的电子传递，导致铁还原菌的丰度增加，铁还原菌与产甲烷古菌竞争，从而降低CH4的排放[92]。而朱永官团队发现来自稻草和粪肥的生物炭可以促进甲烷生成，而来自木屑的生物炭则对甲烷生成无显著影响[93]。进一步的研究发现不同类型的生物炭对产甲烷的不同影响可能是由于氧化还原活性或充放电能力的差异，生物炭表面的官能团(主要是醌类)在促进甲烷生成中发挥了重要作用[93]。这些研究结果为调控土壤甲烷排放提供了理论指导。
4.3 动物瘤胃反刍动物在瘤胃中产生了大量的CH4，这也是大气甲烷的重要来源。据统计，反刍动物产生的甲烷占总全球甲烷排放量的15%[94]。反刍动物瘤胃内的CH4主要由氢营养和甲基营养型产甲烷古菌产生，Methanobrevibacter和Methanomassiliicoccus是其中主要的产甲烷类群[95-97]。研究表明，抑制甲烷生成和提高动物生产力之间存在联系[98]。抑制产甲烷菌可以使瘤胃中的氢最大限度地流向挥发性脂肪酸的生成，将更多的能量导向宿主，提高反刍动物的生产效率，减弱对环境的影响[99]。改变饲料的组成是一种减少甲烷排放的有效策略。在饲料中添加富马酸盐、椰子油、硝酸盐、茶皂素和大豆油等物质可以有效抑制产甲烷古菌活性，减少甲烷排放[100-104]。国外学者发现了一种效果更显著的瘤胃产甲烷菌抑制剂——3-硝基丙醇(3-nitropropanol, 3-NOP)[105]，但它也会导致氢积累，造成能量浪费。因此，我国科学家提出3-NOP与富马酸盐联合使用，可减轻奶牛体内H2的积累，增强对甲烷生成的抑制作用[106]。以上结果为产甲烷古菌与动物营养之间的关系提供了新思路，为调控反刍动物的甲烷排放奠定了基础。
4.4 油藏油藏也是产甲烷古菌的一类重要生境，产甲烷古菌在原油降解和生物气形成过程中发挥着重要作用。石油烃是油藏的主要组成部分，在产甲烷条件下，石油烃主要通过富马酸加成机制被激活[107-108]，这个过程主要由细菌完成，产甲烷古菌主要负责利用烷烃降解后生成的小分子物质产生甲烷。本团队最新的研究表明，存在一类直接降解烷烃产甲烷的古菌——Ca. Methanoliparum[41]。油藏中产甲烷古菌营养类型丰富，乙酸营养型、氢营养型、甲基营养型、甲氧基型和烷基型产甲烷古菌均在油藏中存在。不同温度下油藏环境中占主导的产甲烷古菌不一致。高温油藏中氢营养型产甲烷古菌占主导[109]，而低温油藏中，则同时由氢营养型(如Methanoculleus)和乙酸营养型Methanothrix占主导地位[110]。外来物的添加也会导致油藏中产甲烷途径的改变，如加入针铁矿会促使油藏中主导产甲烷古菌从氢营养型转变为乙酸营养型[111]。培养时间甚至也会影响产甲烷古菌群落结构，陆雅海团队发现随着培养时间的增长，优势产甲烷古菌从乙酸营养型向氢营养型转变[112]。牟伯中团队发现在降解C15–C20正构烷烃的富集培养物中，由Ca. Methanomethyliaceae介导的氢依赖的甲基营养型产甲烷途径发挥了重要作用[113]。本课题组从胜利油田分离出的Methermicoccus shengliensis ZC-1T[8]被发现可以降解甲氧基化合物产甲烷[40]。此外，本课题组还发现烷基型产甲烷古菌Ca. Methanoliparum在油藏中也广泛存在[41]。以上研究结果表明，油藏是一个巨大的产甲烷古菌资源库，可能存在许多目前尚未发现的具有产甲烷功能的古菌。
4.5 其他特殊生境海洋和热液等特殊生境中同样存在产甲烷古菌。海洋中以甲基裂解产甲烷途径为主[114]。热液中以CO2还原产甲烷途径为主[115]。目前已经从海洋和热液分离出Methanothermus fervidus[116]、Methanococcus aeolicus[117]和Methanomicrobium paynteri[118]等多个产甲烷古菌。海洋和热液这些特殊的生态环境还存在大量未培养的产甲烷古菌。如2015年，国外学者在海洋中发现非广古菌门的深古菌也具有潜在的产甲烷能力[20]，2019年，王风平和肖湘团队也从瓜伊马斯盆地热液甲烷渗漏区发现的一个非广古菌门的产甲烷古菌，并将其以古代神话的“哪吒”(Nezhaarchaeota)命名[23]，特殊生境中产甲烷古菌多样性研究，对揭示碳素循环的生物地球化学过程有重要意义。
5 产甲烷古菌的进化早期研究认为产甲烷古菌起源于广古菌门(Euryarchaeota)[119]，但近年来，宏基因组学研究发现产甲烷古菌广泛分布在广古菌门外，推测产甲烷古菌起源于Euryarchaeota、TACK和Asgard古菌的共同祖先[120]。最新的研究提出了这样的假说：在现存古菌的共同祖先(last archaea common ancestor, LACA)出现之前，由甲基化合物产生甲烷的反应已经存在——那可能是一种由非蛋白结构的辅酶F430或类似的以一价镍为核心的催化反应。当LACA出现之时，它已经能够进行多种由蛋白(Mcr及其同系物)催化的产甲烷反应[121]。另一方面，关于产甲烷古菌的原始祖先是CO2还原型还是甲基营养型仍存在争议。国外有学者认为产甲烷古菌起源于一种利用Wood-Ljungdahl途径还原CO2的生物[30]。也有观点认为产甲烷古菌的祖先可能是一种依赖氢的甲基营养性产甲烷古菌[33]。王风平团队提出甲基营养产甲烷古菌是产甲烷古菌祖先[120]。此外，产甲烷古菌一直被认为是一种严格厌氧菌，但在一些有氧环境中检测到了产甲烷古菌，基于抗氧基因含量聚类分析发现，产甲烷古菌可以分为第Ⅰ类和第Ⅱ类产甲烷古菌，它们分别在大氧化事件之前和大氧化事件时进化，后者的抗氧化特性可能有利于产甲烷古菌抗氧能力的进化[122]。
6 互营代谢产甲烷有机物厌氧降解产甲烷，需要厌氧细菌与产甲烷古菌相互依赖和协作。有机物厌氧降解的中间代谢产物如挥发性脂肪酸，进一步降解产生乙酸和氢气的过程，在标准状态下的吉布斯自由能(ΔGθ)为正值，无法自发进行(表 3)。当产甲烷古菌消耗这些H2并使其维持在较低水平(可低至Pa级别)时，脂肪酸等氧化产氢反应的ΔG变为负值，反应可自发进行[123]。这种通过种间氢转移进行的互营代谢，是有机物厌氧降解产甲烷的关键步骤。H2本质是一种电子载体。研究发现，甲酸可以替代H2作为电子载体[124-125]。由于技术手段的限制，种间H2和甲酸转移在互营氧化产甲烷过程中的相对贡献一直不清楚。东秀珠等发现互营细菌Syntrophospora bryantii只能通过种间甲酸转移与产甲烷古菌Methanospirillum hungatei互营降解丁酸产甲烷[126]。此外，还发现了种间甲酸转移对于互营丙酸氧化的重要性[127]。陆雅海团队也证明了二元培养物中Pelotomaculum thermopropionicum和M. conradii通过种间甲酸转移来代谢丙酸产甲烷[128]。汤岳琴团队发现温度是影响2种电子传递方式的重要因素，中温条件下丙酸互营产甲烷过程主要依赖于种间甲酸转移，而高温条件下则更倾向于种间氢转移[129]。电子亦可经厌氧细菌细胞膜上的氧化还原蛋白，直接传递给产甲烷古菌，即种间直接电子传递(direct electron transport between species, DIET)[39]。2012年，刘芳华发现Geobacter metallireducens可将胞内氧化乙醇产生的电子通过DIET传递给产甲烷古菌Methanosarcina barkeri[130]。2015年陆雅海团队发现水稻田土壤中存在DIET介导的互营丁酸产甲烷过程，Geobacteraceae在其中扮演着重要作用[131]。然而，具有DIET功能的物种多样性认识非常有限，细菌主要为Desulfobacula、Desulfobacterium、Deferribacter、Geobacter、Geoalkalibacter、Thauera、Syntrophus和Pseudomonas等属[132]；产甲烷古菌均属于Methanosarcinales，包括Methanothrix harundinacea 8Ac[39](由我国东秀珠团队分离[17])、Methanothrix soehngenii[133]、M. barkeri DSM 800[134]和Methanosarcina mazei[135]。直到2020年，刘芳华团队发现专性甲酸营养型产甲烷古菌Methanobacterium electrotrophus YSL能与G. metallireducens建立基于DIET的互营代谢[136]，首次报道了Methanosarcinales外的产甲烷古菌具有DIET能力。目前的研究认为DIET主要依赖于导电菌毛Pili和细胞色素C，而导电物质可在一定程度上代替Pili和细胞色素C[137-138]。DIET电子传递机制的导电菌毛论和细胞色素论存在一定的争议。一些研究认为导电菌毛对于DIET至关重要[39, 139]。周顺贵团队研究发现Geobacter导电菌毛的组装依赖于一种新型分子伴侣蛋白Spc，为在微生物界中筛选导电菌毛提供了新标准[140]。然而，敲除菌毛(ΔpilB)的G. metallireducens GS-ΔpilB和G. sulfurreducens PCA-ΔpilB之间依然能形成DIET互作关系，表明细胞色素C与DIET具有更直接的关系[141]。随后该团队利用原位光谱电化学技术进一步证实了细胞色素C在DIET中的重要作用[142]。最近他们又证实了细胞色素形成的纳米导线才是胞外电子传递的关键[143]。由此可见，对微生物的DIET机制尚需深入研究。
表 3. 互营有机物降解产甲烷过程中的吉布斯自由能变化[156]
Table 3. Gibbs free energy changes of syntrophic degradation of organic compounds[156]
| Substrates | Reactions | ΔGθ (kJ/mol) | Reference | ||
| Anaerobic oxidation | |||||
| Short chain fatty acids | CH3COOH | CH3COO−+H++2H2O → 2CO2+4H2 | 95 | [157] | |
| CH3CH2COOH | CH3CH2COO−+2H2O → CH3COO−+CO2+3H2 | 72 | |||
| C4H8O2 | C4H7O2−+2H2O → 2CH3COO−+H++2H2 | 49 | |||
| Long chain fatty acids | C18H32O2 | C18H31O2−+16H2O → 9CH3COO−+14H2+8H+ | 272 | [158] | |
| C18H34O2 | C18H33O2−+16H2O → 9CH3COO−+15H2+8H+ | 338 | |||
| C18H36O2 | C18H35O2−+16H2O → 9CH3COO−+16H2+8H+ | 404 | |||
| C16H32O2 | C16H31O2−+14H2O → 8CH3COO−+14H2+7H+ | 353 | |||
| Lactate | CH3CH(OH)COOH | CH3CH(OH)COO−+2H2O → CH3COO−+2H2+H++HCO3− | −4 | [159] | |
| Alcohol | CH3CH2OH | CH3CH2OH+H2O → CH3COO−+2H2+H+ | 9 | [160] | |
| Amino acid | C3H7NO2 | C3H7NO2+2H2O → CH3COO−+2H2+CO2+NH4+ | 10 | [123] | |
| Alkane | C16H34 | 4C16H34+64H2O → 32CH3COO−+68H2+32H+ | 471 | [161] | |
| Aromatics | C6H5COOH | 4C6H5COO−+6H2O → 3CH3COO−+CO2+2H++3H2 | 50 | [123] | |
| C6H6O | C6H6O+5H2O → 3CH3COO−+3H++2H2 | 10 | |||
| Methanogenesis | |||||
| H2 | 4H2+CO2 → CH4+2H2O | −131 | [123] | ||
| HCOOH | 4HCOOH+H2O → CH4+3HCO3− | −130 | [159] | ||
7 产甲烷古菌的应用 7.1 沼气发酵
沼气发酵是产甲烷古菌重要的应用领域之一，其不仅可以提供清洁能源，还减少了废弃物污染及其产生的无序甲烷排放，沼肥还田利用可以改善耕地质量，增加土壤碳汇。我国对沼气发酵的应用可追溯到18世纪80年代[144]。在环境问题日益突出，化石能源越发短缺的大环境下，沼气发酵已被广泛应用于农业、工业以及市政废水废物的排放处理中[144-149]。产甲烷古菌作为沼气发酵的最终执行者，其生物强化作用对调控沼气发酵微生物，提升沼气发酵效率及稳定性具有显著效果。研究表明，添加产甲烷古菌M. barkeri可使高氨氮厌氧污泥的甲烷产量提升59.7%[150]。此外，产甲烷菌系的强化作用亦可提升厌氧消化的反应负荷[151]，改善对高C/N比原料厌氧消化效率[152]，提高对高氨氮原料的耐受能力及甲烷产量[153-155]。据农业农村部不完全统计，截至2021年底，全国累计建成户用沼气池2 000多万户，各类沼气工程近10万处。沼气发酵是实现农业碳中和的重要途径。
7.2 残余油气化传统原油开采技术的开采率不足50%，大部分原油仍然残留在地下[162]。近年来，科学家们提出一种利用产甲烷菌群转化残余油为甲烷的方式，以提高原油开采率，延长油藏寿命[163]。牟伯中团队已经在实验室中成功构建了以细菌Smithella与产甲烷古菌互营作用降解正十六烷烃至正二十烷烃的产甲烷群落体系[107]。本课题组也构建了一个互营降解十六烷烃产甲烷体系[164]。但是这些原油气化体系均存在着培养周期长、转化效率低等缺点。最近，本团队发现了一种够独立降解长链烷基烃的新型产甲烷古菌，它能显著缩短从烷烃到甲烷的时间[41]，这一发现为微生物驱油促使残余油气化打开了一扇窗口。但另一方面，也必须认识到，微生物驱油的理论基础尚不完善，从实验室到现场还需要大量的基础研究。
7.3 光能产甲烷产甲烷古菌利用光电子还原CO2产甲烷，是实现CO2捕获与甲烷化利用的重要途径之一。周顺贵团队利用古菌产甲烷代谢的高效选择性和半导体的光捕获性，构建的M. barkeri- CdS生物-非生物混合光电化学系统，实现了太阳能驱动的CO2或CO还原产CH4[165-166]。改进的M. barkeri-NiCu@CdS系统产甲烷反应速率提升至(79.38±2.83) μmol/(gcat·h)，远高于已知的生物-非生物混合系统以及光催化系统，为太阳能驱动的CO2的能源化利用开辟了新道路[167]。最近，他们提出了“微生物全细胞光敏剂”的概念通过构建了厌氧光合微生物与产甲烷古菌的共培养体系(Rhodopseudomonas palustris-M. barkeri)实现了光能驱动的CO2还原产甲烷[168]。
7.4 非产甲烷功能产甲烷古菌除了产甲烷功能外，还具有非产甲烷功能，例如经遗传改造后的M. maripaludis具有利用CO2产聚β-羟基丁酸(polyhydroxybutyrate, PHB)的功能[169]。这表明产甲烷古菌具有固碳生成高值化合物的应用潜力，但国内鲜有这方面研究的报道。
8 展望(1) 新型产甲烷古菌的分离培养。利用未培养组学的代谢途径预测，结合培养组、高通量分选和定向分离等技术，在特异性序列引导下进行分离获得纯培养物或者高丰度培养物。
(2) 产甲烷代谢的分子机制研究。选择代表性的产甲烷古菌物种，编辑改造产甲烷遗传操作体系，开展产甲烷代谢机理和调控机制研究。
(3) 产甲烷古菌与环境互作。结合同位素标记、原位模拟培养、宏组学测序和关键代谢产物分析，系统评估产甲烷古菌在不同环境中的种群结构与演替，以及生态功能，揭示产甲烷古菌在碳素循环中的生物地球化学作用。
(4) 甲烷生成的示范研究：产甲烷代谢(沼气发酵)是有机废弃物无害化、资源化利用的核心纽带，开发提升沼气发酵效率和速率的新菌种、新工艺和新装备，提高沼气发酵技术的商业价值；开发利用新型的产甲烷技术，如电转化、光催化生物产甲烷等新技术的中试研发，提高产甲烷古菌开发利用的新场景，推动产业化发展。
致谢
感谢农业农村部成都沼气科学研究所的马诗淳博士提供的产甲烷古菌新物种信息，刘刈博士提供的我国沼气工程数据，以及巫可佳和茶桂宏博士为文章修改提出的建议。
References
| [1] | EVANS PN, BOYD JA, LEU AO, WOODCROFT BJ, PARKS DH, HUGENHOLTZ P, TYSON GW. An evolving view of methane metabolism in the archaea. Nature Reviews Microbiology, 2019, 17(4): 219-232. DOI:10.1038/s41579-018-0136-7 |
| [2] | KIRSCHKE S, BOUSQUET P, CIAIS P, SAUNOIS M, CANADELL JG, DLUGOKENCKY EJ, BERGAMASCHI P, BERGMANN D, BLAKE DR, BRUHWILER L. Three decades of global methane sources and sinks. Nature Geoscience, 2013, 6(10): 813-823. DOI:10.1038/ngeo1955 |
| [3] | MYHRE G, SHINDELL D, BRÉON FM, COLLINS W, FUGLESTVEDT J, HUANG J, KOCH D, LAMARQUE JF, LEE D, MENDOZA B, NAKAJIMA T, ROBOCK A, STEPHENS G, TAKEMURA T, ZHANG H. Climate Change 2013–the Physical Science Basis. Cambridge: Cambridge University Press, 2014: 659-740. |
| [4] | SPEECE RE. Anaerobic biotechnology for industrial wastewater treatment. Environmental Science & Technology, 1983, 17(9): 416A-427A. |
| [5] | STEPHENSON M, STICKLAND LH. Hydrogenase: the bacterial formation of methane by the reduction of one-carbon compounds by molecular hydrogen. The Biochemical Journal, 1933, 27(5): 1517-1527. DOI:10.1042/bj0271517 |
| [6] |
ZHOU MJ, YANG XS. Pure cultivation, isolation and identification of Methanosarcina sp.. Microbiology China, 1983, 10(6): 241-244.
(in Chinese) 周孟津, 杨秀山. 甲烷八叠球菌的纯培养、分离和鉴定. 微生物学通报, 1983, 10: 241-244. DOI:10.13344/j.microbiol.china.1983.06.001 |
| [7] | MA K, LIU XL, DONG XZ. Methanobacterium beijingense sp. nov., a novel methanogen isolated from anaerobic digesters. International Journal of Systematic and Evolutionary Microbiology, 2005, 55(Pt 1): 325-329. |
| [8] | CHENG L, QIU TL, YIN XB, WU XL, HU GQ, DENG Y, ZHANG H. Methermicoccus shengliensis gen. nov., sp. nov., a thermophilic, methylotrophic methanogen isolated from oil-production water, and proposal of Methermicoccaceae fam. nov. International Journal of Systematic and Evolutionary Microbiology, 2007, 57(Pt 12): 2964-2969. |
| [9] | ZHU J, LIU X, DONG X. Methanobacterium movens sp. nov. and Methanobacterium flexile sp. nov., isolated from lake sediment. International Journal of Systematic and Evolutionary Microbiology, 2011, 61(Pt 12): 2974-2978. |
| [10] | LÜ Z, LU YH. Methanocella conradii sp. nov., a thermophilic, obligate hydrogenotrophic methanogen, isolated from Chinese rice field soil. PLoS One, 2012, 7(4): e35279. DOI:10.1371/journal.pone.0035279 |
| [11] | LIANG L, SUN Y, DONG Y, AHMAD T, CHEN Y, WANG J, WANG F. Methanococcoides orientis sp. nov., a methylotrophic methanogen isolated from sediment of the East China Sea. International Journal of Systematic and Evolutionary Microbiology, 2022, 72(5): 005384. |
| [12] | TIAN J, WANG Y, DONG X. Methanoculleus hydrogenitrophicus sp. nov., a methanogenic archaeon isolated from wetland soil. International Journal of Systematic and Evolutionary Microbiology, 2010, 60(Pt 9): 2165-2169. |
| [13] | CHENG L, QIU TL, LI X, WANG WD, DENG Y, YIN XB, ZHANG H. Isolation and characterization of Methanoculleus receptaculi sp. nov. from Shengli oil field, China. FEMS Microbiology Letters, 2008, 285(1): 65-71. DOI:10.1111/j.1574-6968.2008.01212.x |
| [14] | CHEN SC, CHEN MF, LAI MC, WENG CY, WU SY, LIN S, YANG TF, CHEN PC. Methanoculleus sediminis sp. nov., a methanogen from sediments near a submarine mud volcano. International Journal of Systematic and Evolutionary Microbiology, 2015, 65(7): 2141-2147. |
| [15] | CHEN SC, TENG NH, LIN YS, LAI MC, CHEN HH, WANG CC. Methanofollis fontis sp. nov., a methanogen isolated from marine sediment near a cold seep at Four-Way Closure Ridge offshore southwestern Taiwan. International Journal of Systematic and Evolutionary Microbiology, 2020, 70(10): 5497-5502. DOI:10.1099/ijsem.0.004440 |
| [16] | SHEN Y, CHEN SC, LAI MC, HUANG HH, CHIU HH, TANG SL, ROGOZIN DY, Degermendzhy AG. Methanolobus halotolerans sp. nov., isolated from the saline Lake Tus in Siberia. International Journal of Systematic and Evolutionary Microbiology, 2020, 70(10): 5586-5593. DOI:10.1099/ijsem.0.004453 |
| [17] | MA K, LIU XL, DONG XZ. Methanosaeta harundinacea sp. nov., a novel acetate-scavenging methanogen isolated from a UASB reactor. International Journal of Systematic and Evolutionary Microbiology, 2006, 56(Pt 1): 127-131. |
| [18] | ZHOU L, LIU X, Dong XZ. Methanospirillum psychrodurum sp. nov., isolated from wetland soil. International Journal of Systematic and Evolutionary Microbiology, 2014, 64(Pt 2): 638-641. |
| [19] | CHENG L, DAI LR, LI X, ZHANG H, LU YH. Isolation and characterization of Methanothermobacter crinale sp. nov., a novel hydrogenotrophic methanogen from the Shengli oil field. Applied and Environmental Microbiology, 2011, 77(15): 5212-5219. DOI:10.1128/AEM.00210-11 |
| [20] | EVANS PN, PARKS DH, CHADWICK GL, ROBBINS SJ, ORPHAN VJ, GOLDING SD, TYSON GW. Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics. Science, 2015, 350(6259): 434-438. DOI:10.1126/science.aac7745 |
| [21] | WANG YL, HUA ZS, GOH KM, EVANS P, LIU L, MAO YP, HUGENHOLTZ P, TYSON G, LI WJ, ZHANG T. Further expansion of methane metabolism in the archaea. bioRxiv, 2018: 312082. |
| [22] | McKAY LJ, DLAKIĆ M, FIELDS MW, DELMONT TO, EREN AM, JAY ZJ, KLINGELSMITH KB, RUSCH DB, INSKEEP WP. Co-occurring genomic capacity for anaerobic methane and dissimilatory sulfur metabolisms discovered in the Korarchaeota. Nature Microbiology, 2019, 4(4): 614-622. DOI:10.1038/s41564-019-0362-4 |
| [23] | WANG YZ, WEGENER G, HOU JL, WANG FP, XIAO X. Expanding anaerobic alkane metabolism in the domain of archaea. Nature Microbiology, 2019, 4(4): 595-602. DOI:10.1038/s41564-019-0364-2 |
| [24] | BORREL G, HARRIS HMB, TOTTEY W, MIHAJLOVSKI A, PARISOT N, PEYRETAILLADE E, PEYRET P, GRIBALDO S, O'TOOLE PW, BRUGÈRE JF. Genome sequence of "Candidatus Methanomethylophilus alvus" Mx1201, a methanogenic archaeon from the human gut belonging to a seventh order of methanogens. Journal of Bacteriology, 2012, 194(24): 6944-6945. DOI:10.1128/JB.01867-12 |
| [25] | LANG K, SCHULDES J, KLINGL A, POEHLEIN A, DANIEL R, BRUNEA A. New mode of energy metabolism in the seventh order of methanogens as revealed by comparative genome analysis of "Candidatus Methanoplasma termitum". Applied and Environmental Microbiology, 2015, 81(4): 1338-1352. DOI:10.1128/AEM.03389-14 |
| [26] | ⅡNO T, TAMAKI H, TAMAZAWA S, UENO Y, OHKUMA M, SUZUKI KI, IGARASHI Y, HARUTA S. Candidatus Methanogranum caenicola: a novel methanogen from the anaerobic digested sludge, and proposal of Methanomassiliicoccaceae fam. nov. and Methanomassiliicoccales ord. nov., for a methanogenic lineage of the class Thermoplasmata. Microbes and Environments, 2013, 28(2): 244-250. |
| [27] | GILROY R, RAVI A, GETINO M, PURSLEY I, HORTON DL, ALIKHAN NF, BAKER D, GHARBI K, HALL N, WATSON M, ADRIAENSSENS EM, FOSTER-NYARKO E, JARJU S, SECKA A, ANTONIO M, OREN A, CHAUDHURI RR, la RAGIONE R, HILDEBRAND F, PALLEN MJ. Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture. PeerJ, 2021, 9: e10941. DOI:10.7717/peerj.10941 |
| [28] | OU YF, DONG HP, MCILROY SJ, CROWE SA, HALLAM SJ, HAN P, KALLMEYER J, SIMISTER RL, VUILLEMIN A, LEU AO, LIU ZF, ZHENG YL, SUN QL, LIU M, TYSON GW, HOU LJ. Expanding the phylogenetic distribution of cytochrome b-containing methanogenic archaea sheds light on the evolution of methanogenesis. The ISME Journal, 2022, 16(10): 2373-2387. DOI:10.1038/s41396-022-01281-0 |
| [29] | VANWONTERGHEM I, EVANS PN, PARKS DH, JENSEN PD, WOODCROFT BJ, HUGENHOLTZ P, TYSON GW. Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota. Nature Microbiology, 2016, 1: 16170. DOI:10.1038/nmicrobiol.2016.170 |
| [30] | BERGHUIS BA, YU FB, SCHULZ F, BLAINEY PC, WOYKE T, QUAKE SR. Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens. Proceedings of the National Academy of Sciences of the United States of America, 2019, 116(11): 5037-5044. DOI:10.1073/pnas.1815631116 |
| [31] | SOROKIN DY, MAKAROVA KS, ABBAS B, FERRER M, GOLYSHIN PN, GALINSKI EA, CIORDIA S, MENA MC, MERKEL AY, WOLF YI, van LOOSDRECHT MCM, KOONIN EV. Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis. Nature Microbiology, 2017, 2: 17081. DOI:10.1038/nmicrobiol.2017.81 |
| [32] | NOBU MK, NARIHIRO T, KURODA K, MEI R, LIU WT. Chasing the elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious methyl-reducing methanogen. The ISME Journal, 2016, 10(10): 2478-2487. DOI:10.1038/ismej.2016.33 |
| [33] | BORREL G, ADAM PS, MCKAY LJ, CHEN LX, SIERRA-GARCÍA IN, SIEBER CMK, LETOURNEUR Q, GHOZLANE A, ANDERSEN GL, LI WJ, HALLAM SJ, MUYZER G, de OLIVEIRA VM, INSKEEP WP, BANFIELD JF, GRIBALDO S. Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea. Nature Microbiology, 2019, 4(4): 603-613. DOI:10.1038/s41564-019-0363-3 |
| [34] | MONDAV R, WOODCROFT BJ, KIM EH, MCCALLEY CK, HODGKINS SB, CRILL PM, CHANTON J, HURST GB, VERBERKMOES NC, SALESKA SR, HUGENHOLTZ P, RICH VI, TYSON GW. Discovery of a novel methanogen prevalent in thawing permafrost. Nature Communications, 2014, 5: 3212. DOI:10.1038/ncomms4212 |
| [35] | LIU YF, CHEN J, ZARAMELA LS, WANG LY, MBADINGA SM, HOU ZW, WU XL, GU JD, ZENGLER K, MU BZ. Genomic and transcriptomic evidence supports methane metabolism in Archaeoglobi. mSystems, 2020, 5(2): e00651-e00619. |
| [36] |
CHENG L, ZHENG ZZ, WANG C, ZHANG H. Recent advances in methanogens. Microbiology China, 2016, 43(5): 1143-1164.
(in Chinese) 承磊, 郑珍珍, 王聪, 张辉. 产甲烷古菌研究进展. 微生物学通报, 2016, 43(5): 1143-1164. DOI:10.13344/j.microbiol.china.150993 |
| [37] | LYU Z, SHAO NN, AKINYEMI T, WHITMAN WB. Methanogenesis. Current Biology: CB, 2018, 28(13): R727-R732. DOI:10.1016/j.cub.2018.05.021 |
| [38] | DRIDI B, FARDEAU ML, OLLIVIER B, RAOULT D, DRANCOURT M. Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces. International Journal of Systematic and Evolutionary Microbiology, 2012, 62(Pt 8): 1902-1907. |
| [39] | ROTARU AE, SHRESTHA PM, LIU FH, SHRESTHA M, SHRESTHA D, EMBREE M, ZENGLER K, WARDMAN C, NEVIN KP, LOVLEY DR. A new model for electron flow during anaerobic digestion: direct interspecies electron transfer to Methanosaeta for the reduction of carbon dioxide to methane. Energy & Environmental Science, 2014, 7(1): 408-415. |
| [40] | MAYUMI D, MOCHIMARU H, TAMAKI H, YAMAMOTO K, YOSHIOKA H, SUZUKI Y, KAMAGATA Y, SAKATA S. Methane production from coal by a single methanogen. Science, 2016, 354(6309): 222-225. DOI:10.1126/science.aaf8821 |
| [41] | ZHOU Z, ZHANG CJ, LIU PF, FU L, LASO-PÉREZ R, YANG L, BAI LP, LI J, YANG M, LIN JZ, WANG WD, WEGENER G, LI M, CHENG L. Non-syntrophic methanogenic hydrocarbon degradation by an archaeal species. Nature, 2022, 601(7892): 257-262. DOI:10.1038/s41586-021-04235-2 |
| [42] | DINESH G, SHALVARJIAN KATIE E, NAYAK DIPTI D. An archaea-specific c-type cytochrome maturation machinery is crucial for methanogenesis in Methanosarcina acetivorans. eLife, 2022, 11: e76970. DOI:10.7554/eLife.76970 |
| [43] | FINK C, BEBLAWY S, ENKERLIN AM, MÜHLING L, ANGENENT LT, MOLITOR B. A shuttle-vector system allows heterologous gene expression in the thermophilic methanogen Methanothermobacter thermautotrophicus ΔH. mBio, 2021, 12(6): e0276621. DOI:10.1128/mBio.02766-21 |
| [44] | BUAN N, KULKARNI G, METCALF W. Genetic methods for Methanosarcina species. Methods in Enzymology, 2011, 494: 23-42. |
| [45] | ALDRIDGE J, CARR S, WEBER KA, BUAN NR. Anaerobic production of isoprene by engineered Methanosarcina species archaea. Applied and Environmental Microbiology, 2021, 87(6): e02417-e02420. |
| [46] | MOORE BC, LEIGH JA. Markerless mutagenesis in Methanococcus maripaludis demonstrates roles for alanine dehydrogenase, alanine racemase, and alanine permease. Journal of Bacteriology, 2005, 187(3): 972-979. DOI:10.1128/JB.187.3.972-979.2005 |
| [47] | LI J, ZHANG LY, XU Q, ZHANG WT, LI ZH, CHEN L, DONG XZ. CRISPR-Cas9 toolkit for genome editing in an autotrophic CO2-fixing methanogenic archaeon. Microbiology Spectrum, 2022, 10(4): e0116522. DOI:10.1128/spectrum.01165-22 |
| [48] | QI L, YUE L, FENG DQ, QI FX, LI J, DONG XZ. Genome-wide mRNA processing in methanogenic archaea reveals post-transcriptional regulation of ribosomal protein synthesis. Nucleic Acids Research, 2017, 45(12): 7285-7298. DOI:10.1093/nar/gkx454 |
| [49] | JIA J, LI J, QI L, LI LY, YUE L, DONG XZ. Post-transcriptional regulation is involved in the cold-active methanol-based methanogenic pathway of a psychrophilic methanogen. Environmental Microbiology, 2021, 23(7): 3773-3788. DOI:10.1111/1462-2920.15420 |
| [50] | CAO Y, LI J, JIANG N, DONG XZ. Mechanism for stabilizing mRNAs involved in methanol-dependent methanogenesis of cold-adaptive Methanosarcina mazei zm-15. Applied and Environmental Microbiology, 2014, 80(4): 1291-1298. DOI:10.1128/AEM.03495-13 |
| [51] | QI L, LI J, JIA J, YUE L, DONG XZ. Comprehensive analysis of the pre-ribosomal RNA maturation pathway in a methanoarchaeon exposes the conserved circularization and linearization mode in archaea. RNA Biology, 2020, 17(10): 1427-1441. DOI:10.1080/15476286.2020.1771946 |
| [52] | ZHANG B, YUE L, ZHOU LG, QI L, LI J, DONG XZ. Conserved TRAM domain functions as an archaeal cold shock protein via RNA chaperone activity. Frontiers in Microbiology, 2017, 8: 1597. DOI:10.3389/fmicb.2017.01597 |
| [53] | LI J, ZHANG B, ZHOU LG, QI L, YUE L, ZHANG WT, CHENG HC, WHITMAN WB, DONG XZ. The archaeal RNA chaperone TRAM0076 shapes the transcriptome and optimizes the growth of Methanococcus maripaludis. PLoS Genetics, 2019, 15(8): e1008328. DOI:10.1371/journal.pgen.1008328 |
| [54] | YUE L, LI J, ZHANG B, QI L, LI ZH, ZHAO FQ, LI LY, ZHENG XW, DONG XZ. The conserved ribonuclease aCPSF1 triggers genome-wide transcription termination of archaea via a 3'-end cleavage mode. Nucleic Acids Research, 2020, 48(17): 9589-9605. DOI:10.1093/nar/gkaa702 |
| [55] | LI J, ZHENG XW, LI LY, ZHANG SJ, REN MF, HUANG L, DONG XZ. The archaeal transcription termination factor aCPSF1 is a robust phylogenetic marker for archaeal taxonomy. Microbiology Spectrum, 2021, 9(3): e0153921. DOI:10.1128/spectrum.01539-21 |
| [56] | LI J, YUE L, LI ZH, ZHANG WT, ZHANG B, ZHAO FQ, DONG XZ. aCPSF1 cooperates with terminator U-tract to dictate archaeal transcription termination efficacy. eLife, 2021, 10: e70464. DOI:10.7554/eLife.70464 |
| [57] | ZENG ZR, CHEN HH, YANG H, CHEN YF, YANG W, FENG X, PEI HY, WELANDER PV. Identification of a protein responsible for the synthesis of archaeal membrane-spanning GDGT lipids. Nature Communications, 2022, 13: 1545. DOI:10.1038/s41467-022-29264-x |
| [58] | ZHANG JZ, LI T, HONG ZL, MA CF, FANG XT, ZHENG FF, TENG WK, ZHANG CL, SI T. Biosynthesis of hybrid neutral lipids with archaeal and eukaryotic characteristics in engineered Saccharomyces cerevisiae. Angewandte Chemie (International Ed in English), 2023, 62(4): e202214344. |
| [59] | BRIDGHAM SD, CADILLO-QUIROZ H, KELLER JK, ZHUANG QL. Methane emissions from wetlands: biogeochemical, microbial, and modeling perspectives from local to global scales. Global Change Biology, 2013, 19(5): 1325-1346. DOI:10.1111/gcb.12131 |
| [60] | ZHANG YF, MA AZ, ZHUANG GQ, ZHUANG XL. The acetotrophic pathway dominates methane production in Zoige alpine wetland coexisting with hydrogenotrophic pathway. Scientific Reports, 2019, 9: 9141. DOI:10.1038/s41598-019-45590-5 |
| [61] | ZHANG GS, TIAN JQ, JIANG N, GUO XP, WANG YF, DONG XZ. Methanogen community in Zoige wetland of Tibetan Plateau and phenotypic characterization of a dominant uncultured methanogen cluster ZC-I. Environmental Microbiology, 2008, 10(7): 1850-1860. DOI:10.1111/j.1462-2920.2008.01606.x |
| [62] | YANG SZ, LIEBNER S, WINKEL M, ALAWI M, HORN F, DÖRFER C, OLLIVIER JF, HE J, JIN H, KÜHN P, SCHLOTER M, SCHOLTEN T, WAGNER D. In-depth analysis of core methanogenic communities from high elevation permafrost-affected wetlands. Soil Biology & Biochemistry, 2017, 111: 66-77. |
| [63] | SCHÖNHEIT P, KRISTJANSSON JK, THAUER RK. Kinetic mechanism for the ability of sulfate reducers to out-compete methanogens for acetate. Archives of Microbiology, 1982, 132(3): 285-288. DOI:10.1007/BF00407967 |
| [64] | ZHANG CJ, PAN J, LIU Y, DUAN CH, LI M. Genomic and transcriptomic insights into methanogenesis potential of novel methanogens from mangrove sediments. Microbiome, 2020, 8(1): 94. DOI:10.1186/s40168-020-00876-z |
| [65] | LI W, GUAN W, CHEN H, LIAO BW, HU J, PENG CH, RUI JP, TIAN JQ, ZHU D, HE YX. Archaeal communities in the sediments of different mangrove stands at Dongzhaigang, China. Journal of Soils and Sediments, 2016, 16(7): 1995-2004. DOI:10.1007/s11368-016-1427-0 |
| [66] | LI W, GUAN W, CHEN H, LIAO B, HU J, RUI JP, PENG C, ZHU D, HE YX, TIAN JQ. Variations of sediment archaea communities in different distribution areas of Bruguiera gymnoihiza mangrove in Dongzhaigang, China. Polish Journal of Environmental Studies, 2019, 28(5): 3343-3352. DOI:10.15244/pjoes/90030 |
| [67] | DENG Y, LIU P, CONRAD R. Effect of temperature on the microbial community responsible for methane production in alkaline NamCo wetland soil. Soil Biology and Biochemistry, 2019, 132: 69-79. DOI:10.1016/j.soilbio.2019.01.024 |
| [68] | LIU YQ, YAO TD, GLEIXNER G, CLAUS P, CONRAD R. Methanogenic pathways, 13C isotope fractionation, and archaeal community composition in lake sediments and wetland soils on the Tibetan Plateau. Journal of Geophysical Research: Biogeosciences, 2013, 118(2): 650-664. DOI:10.1002/jgrg.20055 |
| [69] | LIU DY, DING WX, JIA ZJ, CAI ZC. The impact of dissolved organic carbon on the spatial variability of methanogenic archaea communities in natural wetland ecosystems across China. Applied Microbiology and Biotechnology, 2012, 96(1): 253-263. DOI:10.1007/s00253-011-3842-x |
| [70] | LIU DY, DING W, JIA Z, CAI Z. Relation between methanogenic archaea and methane production potential in selected natural wetland ecosystems across China. Biogeosciences, 2011, 8: 329-338. DOI:10.5194/bg-8-329-2011 |
| [71] | LI JJ, XIAO LL, ZHENG SL, ZHANG YC, LUO M, TONG C, XU HD, TAN Y, LIU J, WANG OM, LIU FH. A new insight into the strategy for methane production affected by conductive carbon cloth in wetland soil: beneficial to acetoclastic methanogenesis instead of CO2 reduction. The Science of the Total Environment, 2018, 643: 1024-1030. DOI:10.1016/j.scitotenv.2018.06.271 |
| [72] |
JIANG N, CHEN ZJ, CAO Y, TIAN JQ, WANG YF, DONG XZ. Methanogenic archaea and their mediated methanogenic pathways in cold wetland. Microbiology China, 2013, 40(1): 137-145.
(in Chinese) 蒋娜, 陈紫娟, 曹轶, 田建卿, 王艳芬, 东秀珠. 低温湿地甲烷古菌及其介导的甲烷产生途径. 微生物学通报, 2013, 40(1): 137-145. DOI:10.13344/j.microbiol.china.2013.01.015 |
| [73] | LIN YX, LIU DY, DING WX, KANG H, FREEMAN C, YUAN JJ, XIANG J. Substrate sources regulate spatial variation of metabolically active methanogens from two contrasting freshwater wetlands. Applied Microbiology and Biotechnology, 2015, 99(24): 10779-10791. DOI:10.1007/s00253-015-6912-7 |
| [74] | SCHINK B, ZEIKUS JG. Microbial methanol formation: a major end product of pectin metabolism. Current Microbiology, 1980, 4(6): 387-389. DOI:10.1007/BF02605383 |
| [75] | ZHANG Z, POULTER B, FELDMAN AF, YING Q, CIAIS P, PENG SS, LI X. Recent intensification of wetland methane feedback. Nature Climate Change, 2023: 1-4. |
| [76] | BAO T, JIA GS, XU XY. Weakening greenhouse gas sink of pristine wetlands under warming. Nature Climate Change, 2023: 1-8. |
| [77] | PENG SS, LIN X, THOMPSON RL, XI Y, LIU G, HAUGLUSTAINE D, LAN X, POULTER B, RAMONET M, SAUNOIS M, YIN Y, ZHANG Z, ZHENG B, CIAIS P. Wetland emission and atmospheric sink changes explain methane growth in 2020. Nature, 2022, 612(7940): 477-482. DOI:10.1038/s41586-022-05447-w |
| [78] | YAN XY, AKIYAMA H, YAGI K, AKIMOTO H. Global estimations of the inventory and mitigation potential of methane emissions from rice cultivation conducted using the 2006 intergovernmental panel on climate change guidelines. Global Biogeochemical Cycles, 2009, 23(2): 20-23. |
| [79] |
MIN H, CHEN MC, QIAN ZS. Studies on characteristics of release of methane as well as biological mechanisms in rice paddy soil. Journal of Ecology and Rural Environment, 1993, 9(S1): 28-32.
(in Chinese) 闵航, 陈美慈, 钱泽澍. 水稻田的甲烷释放特性及其生物学机理. 生态与农村环境学报, 1993, 9(S1): 28-32. |
| [80] | KRÜGER M, FRENZEL P, KEMNITZ D, CONRAD R. Activity, structure and dynamics of the methanogenic archaeal community in a flooded Italian rice field. FEMS Microbiology Ecology, 2005, 51(3): 323-331. DOI:10.1016/j.femsec.2004.09.004 |
| [81] | YAO H, CONRAD R, WASSMANN R, NEUE HU. Effect of soil characteristics on sequential reduction and methane production in sixteen rice paddy soils from China, the Philippines, and Italy. Biogeochemistry, 1999, 47(3): 269-295. DOI:10.1007/BF00992910 |
| [82] | LU YH, LUEDERS T, FRIEDRICH MW, CONRAD R. Detecting active methanogenic populations on rice roots using stable isotope probing. Environmental Microbiology, 2005, 7(3): 326-336. DOI:10.1111/j.1462-2920.2005.00697.x |
| [83] | LIU FH, CONRAD R. Thermoanaerobacteriaceae oxidize acetate in methanogenic rice field soil at 50 ℃. Environmental Microbiology, 2010, 12(8): 2341-2354. |
| [84] | WU XL, FRIEDRICH MW, CONRAD R. Diversity and ubiquity of thermophilic methanogenic archaea in temperate anoxic soils. Environmental Microbiology, 2006, 8(3): 394-404. DOI:10.1111/j.1462-2920.2005.00904.x |
| [85] | MA K, CONRAD R, LU YH. Responses of methanogen mcrA genes and their transcripts to an alternate dry/wet cycle of paddy field soil. Applied and Environmental Microbiology, 2012, 78(2): 445-454. DOI:10.1128/AEM.06934-11 |
| [86] | LU YH, CONRAD R. In situ stable isotope probing of methanogenic archaea in the rice rhizosphere. Science, 2005, 309(5737): 1088-1090. DOI:10.1126/science.1113435 |
| [87] | YUAN YL, CONRAD R, LU YH. Responses of methanogenic archaeal community to oxygen exposure in rice field soil. Environmental Microbiology Reports, 2009, 1(5): 347-354. DOI:10.1111/j.1758-2229.2009.00036.x |
| [88] | YUAN Q, LU YH. Response of methanogenic archaeal community to nitrate addition in rice field soil. Environmental Microbiology Reports, 2009, 1(5): 362-369. DOI:10.1111/j.1758-2229.2009.00065.x |
| [89] | MA K, LU YH. Regulation of microbial methane production and oxidation by intermittent drainage in rice field soil. FEMS Microbiology Ecology, 2011, 75(3): 446-456. DOI:10.1111/j.1574-6941.2010.01018.x |
| [90] | PENG JJ, LÜ Z, RUI JP, LU YH. Dynamics of the methanogenic archaeal community during plant residue decomposition in an anoxic rice field soil. Applied and Environmental Microbiology, 2008, 74(9): 2894-2901. DOI:10.1128/AEM.00070-08 |
| [91] | MA KE, QIU QF, LU YH. Microbial mechanism for rice variety control on methane emission from rice field soil. Global Change Biology, 2010, 16(11): 3085-3095. |
| [92] | WANG N, CHANG ZZ, XUE XM, YU JG, SHI XX, MA LQ, LI HB. Biochar decreases nitrogen oxide and enhances methane emissions via altering microbial community composition of anaerobic paddy soil. Science of the Total Environment, 2017, 581/582: 689-696. DOI:10.1016/j.scitotenv.2016.12.181 |
| [93] | YUAN HY, DING LJ, ZAMA EF, LIU PP, HOZZEIN WN, ZHU YG. Biochar modulates methanogenesis through electron syntrophy of microorganisms with ethanol as a substrate. Environmental Science & Technology, 2018, 52(21): 12198-12207. |
| [94] | YUSUF RO, NOOR ZZ, ABBA AH, HASSAN MAA, DIN MFM. Methane emission by sectors: a comprehensive review of emission sources and mitigation methods. Renewable and Sustainable Energy Reviews, 2012, 16(7): 5059-5070. DOI:10.1016/j.rser.2012.04.008 |
| [95] | HUANG XD, TAN HY, LONG RJ, LIANG JB, WRIGHT AD G. Comparison of methanogen diversity of yak (Bos grunniens) and cattle (Bos taurus) from the Qinghai-Tibetan Plateau, China. BMC Microbiology, 2012, 12: 237. DOI:10.1186/1471-2180-12-237 |
| [96] | HUANG JQ, LI YJ. Rumen methanogen and protozoal communities of Tibetan sheep and Gansu Alpine Finewool sheep grazing on the Qinghai-Tibetan Plateau, China. BMC Microbiology, 2018, 18(1): 212. DOI:10.1186/s12866-018-1351-0 |
| [97] | XING BS, HAN YL, WANG XC, WEN JW, CAO SF, ZHANG KD, LI Q, YUAN HL. Persistent action of cow rumen microorganisms in enhancing biodegradation of wheat straw by rumen fermentation. The Science of the Total Environment, 2020, 715: 136529. DOI:10.1016/j.scitotenv.2020.136529 |
| [98] | HRISTOV AN, OH J, GIALLONGO F, FREDERICK TW, HARPER MT, WEEKS HL, BRANCO AF, MOATE PJ, DEIGHTON MH, KINDERMANN M, DUVAL S. An inhibitor persistently decreased enteric methane emission from dairy cows with no negative effect on milk production. Proceedings of the National Academy of Sciences of the United States of America, 2015, 112(34): 10663-10668. DOI:10.1073/pnas.1504124112 |
| [99] | UNGERFELD EM. Shifts in metabolic hydrogen sinks in the methanogenesis-inhibited ruminal fermentation: a meta-analysis. Frontiers in Microbiology, 2015, 6: 37. |
| [100] | YANG CJ, MAO SY, LONG LM, ZHU WY. Effect of disodium fumarate on microbial abundance, ruminal fermentation and methane emission in goats under different forage: concentrate ratios. Animal: an International Journal of Animal Bioscience, 2012, 6(11): 1788-1794. DOI:10.1017/S1751731112000857 |
| [101] | DING XZ, LONG R, ZHANG Q, HUANG XD, GUO XS, MI J. Reducing methane emissions and the methanogen population in the rumen of Tibetan sheep by dietary supplementation with coconut oil. Tropical Animal Health and Production, 2012, 44: 1541-1545. DOI:10.1007/s11250-012-0103-7 |
| [102] | GUO WS, SCHAEFER DM, GUO XX, REN LP, MENG QX. Use of nitrate-nitrogen as a sole dietary nitrogen source to inhibit ruminal methanogenesis and to improve microbial nitrogen synthesis in vitro. Asian-Australasian Journal of Animal Sciences, 2009, 22(4): 542-549. DOI:10.5713/ajas.2009.80361 |
| [103] | ZHAO LP, MENG QX, LI Y, WU H, HUO YL, ZHANG XZ, ZHOU ZM. Nitrate decreases ruminal methane production with slight changes to ruminal methanogen composition of nitrate-adapted steers. BMC Microbiology, 2018, 18(1): 21. DOI:10.1186/s12866-018-1164-1 |
| [104] | MAO HL, WANG JK, ZHOU YY, LIU JX. Effects of addition of tea saponins and soybean oil on methane production, fermentation and microbial population in the rumen of growing lambs. Livestock Science, 2010, 129(1/2/3): 56-62. |
| [105] | van WESEMAEL D, VANDAELE L, AMPE B, CATTRYSSE H, DUVAL S, KINDERMANN M, FIEVEZ V, de CAMPENEERE S, PEIREN N. Reducing enteric methane emissions from dairy cattle: two ways to supplement 3-nitrooxypropanol. Journal of Dairy Science, 2019, 102(2): 1780-1787. DOI:10.3168/jds.2018-14534 |
| [106] | LIU ZH, WANG K, NAN XM, CAI M, YANG L, XIONG BH, ZHAO YG. Synergistic effects of 3-nitrooxypropanol with fumarate in the regulation of propionate formation and methanogenesis in dairy cows in vitro. Applied and Environmental Microbiology, 2022, 88(6): e0190821. DOI:10.1128/aem.01908-21 |
| [107] | JI JH, LIU YF, ZHOU L, MBADINGA SM, PAN P, CHEN J, LIU JF, YANG SZ, SAND W, GU JD, MU BZ. Methanogenic degradation of long n-alkanes requires fumarate-dependent activation. Applied and Environmental Microbiology, 2019, 85(16): e00985-e00919. |
| [108] | CHEN J, LIU YF, ZHOU L, MBADINGA SM, YANG T, ZHOU J, LIU JF, YANG SZ, GU JD, MU BZ. Methanogenic degradation of branched alkanes in enrichment cultures of production water from a high-temperature petroleum reservoir. Applied Microbiology and Biotechnology, 2019, 103(5): 2391-2401. DOI:10.1007/s00253-018-09574-1 |
| [109] | MBADINGA SM, LI KP, ZHOU L, WANG LY, YANG SZ, LIU JF, GU JD, MU BZ. Analysis of alkane-dependent methanogenic community derived from production water of a high-temperature petroleum reservoir. Applied Microbiology and Biotechnology, 2012, 96(2): 531-542. DOI:10.1007/s00253-011-3828-8 |
| [110] | LIU JF, LU YW, ZHOU L, LI W, HOU ZW, YANG SZ, WU XL, GU JD, MU BZ. Simultaneous detection of transcribed functional assA gene and the corresponding metabolites of linear alkanes (C4, C5, and C7) in production water of a low-temperature oil reservoir. Science of the Total Environment, 2020, 746: 141290. DOI:10.1016/j.scitotenv.2020.141290 |
| [111] | PAN P, HONG B, MBADINGA SM, WANG LY, LIU JF, YANG SZ, GU JD, MU BZ. Iron oxides alter methanogenic pathways of acetate in production water of high-temperature petroleum reservoir. Applied Microbiology and Biotechnology, 2017, 101(18): 7053-7063. DOI:10.1007/s00253-017-8422-2 |
| [112] | CHENG L, RUI JP, LI Q, ZHANG H, LU YH. Enrichment and dynamics of novel syntrophs in a methanogenic hexadecane-degrading culture from a Chinese oilfield. FEMS Microbiology Ecology, 2013, 83(3): 757-766. DOI:10.1111/1574-6941.12031 |
| [113] | LIU YF, CHEN J, LIU ZL, HOU ZW, LIANG B, WANG LY, ZHOU L, SHOU LB, LIN DD, YANG SZ, LIU JF, WU XL, GU JD, MU BZ. Long-term cultivation and meta-omics reveal methylotrophic methanogenesis in hydrocarbon-impacted habitats. Engineering, 2022. |
| [114] | XU L, ZHUANG GC, MONTGOMERY A, LIANG QY, JOYE SB, WANG FP. Methyl-compounds driven benthic carbon cycling in the sulfate-reducing sediments of South China Sea. Environmental Microbiology, 2021, 23(2): 641-651. DOI:10.1111/1462-2920.15110 |
| [115] | ZHOU ZH, WANG CK, LUO YQ. Meta-analysis of the impacts of global change factors on soil microbial diversity and functionality. Nature Communications, 2020, 11: 3072. DOI:10.1038/s41467-020-16881-7 |
| [116] | STETTER KO, THOMM M, WINTER J, WILDGRUBER G, HUBER H, ZILLIG W, JANÉ-COVIC D, KNIG H, PALM P, WUNDERL S. Methanothermus fervidus, sp. nov., a novel extremely thermophilic methanogen isolated from an Icelandic hot spring. Zentralblatt für Bakteriologie Mikrobiologie und Hygiene: I. Abt. Originale C: Allgemeine, angewandte und ökologische Mikrobiologie, 1981, 2(2): 166-178. DOI:10.1016/S0721-9571(81)80038-5 |
| [117] | KENDALL MM, LIU YT, SIEPRAWSKA-LUPA M, STETTER KO, WHITMAN WB, BOONE DR. Methanococcus aeolicus sp. nov., a mesophilic, methanogenic archaeon from shallow and deep marine sediments. International Journal of Systematic and Evolutionary Microbiology, 2006, 56(Pt 7): 1525-1529. |
| [118] | RIVARD CJ, HENSON JM, THOMAS MV, SMITH PH. Isolation and characterization of Methanomicrobium paynteri sp. nov., a mesophilic methanogen isolated from marine sediments. Applied and Environmental Microbiology, 1983, 46(2): 484-490. DOI:10.1128/aem.46.2.484-490.1983 |
| [119] | BROCHIER C, FORTERRE P, GRIBALDO S. Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox. Genome Biology, 2004, 5(3): R17. DOI:10.1186/gb-2004-5-3-r17 |
| [120] | WANG YZ, WEGENER G, WILLIAMS TA, XIE RZ, HOU JL, WANG FP, XIAO X. A methylotrophic origin of methanogenesis and early divergence of anaerobic multicarbon alkane metabolism. Science Advances, 2021, 7(7): eabd7180. DOI:10.1126/sciadv.abd7180 |
| [121] | MEI R, KANEKO M, IMACHI H, NOBU MK. The origin and evolution of methanogenesis and archaea are intertwined. Proceedings of the National Academy of Sciences of the United States of America Nexus, 2023, 2(2): pgad023. |
| [122] | LYU Z, LU YH. Metabolic shift at the class level sheds light on adaptation of methanogens to oxidative environments. The ISME Journal, 2018, 12(2): 411-423. DOI:10.1038/ismej.2017.173 |
| [123] | SCHINK B. Energetics of syntrophic cooperation in methanogenic degradation. Microbiology and Molecular Biology Reviews: MMBR, 1997, 61(2): 262-280. |
| [124] | THIELE JH, CHARTRAIN M, ZEIKUS JG. Control of interspecies electron flow during anaerobic digestion: role of floc formation in syntrophic methanogenesis. Applied and Environmental Microbiology, 1988, 54(1): 10-19. DOI:10.1128/aem.54.1.10-19.1988 |
| [125] | BOONE DR, JOHNSON RL, LIU Y. Diffusion of the interspecies electron carriers H2 and formate in methanogenic ecosystems and its implications in the measurement of Km for H2 or formate uptake. Applied and Environmental Microbiology, 1989, 55(7): 1735-1741. DOI:10.1128/aem.55.7.1735-1741.1989 |
| [126] | DONG XZ, CHENG G, STAMS AM. Butyrate oxidation by Syntrophospora bryantii in co-culture with different methanogens and in pure culture with pentenoate as electron acceptor. Applied Microbiology and Biotechnology, 1994, 42(4): 647-652. DOI:10.1007/BF00173934 |
| [127] | DONG XZ, PLUGGE CM, STAMS AJ. Anaerobic degradation of propionate by a mesophilic acetogenic bacterium in coculture and triculture with different methanogens. Applied and Environmental Microbiology, 1994, 60(8): 2834-2838. DOI:10.1128/aem.60.8.2834-2838.1994 |
| [128] | LIU PF, LU YH. Concerted metabolic shifts give new insights into the syntrophic mechanism between propionate-fermenting Pelotomaculum thermopropionicum and hydrogenotrophic Methanocella conradii. Frontiers in Microbiology, 2018, 9: 1551. DOI:10.3389/fmicb.2018.01551 |
| [129] | CHEN YT, ZENG Y, WANG HZ, ZHENG D, KAMAGATA Y, NARIHIRO T, NOBU MK, TANG YQ. Different interspecies electron transfer patterns during mesophilic and thermophilic syntrophic propionate degradation in chemostats. Microbial Ecology, 2020, 80(1): 120-132. DOI:10.1007/s00248-020-01485-x |
| [130] | LIU FH, ROTARU AE, SHRESTHA PM, MALVANKAR NS, NEVIN KP, LOVLEY DR. Promoting direct interspecies electron transfer with activated carbon. Energy & Environmental Science, 2012, 5: 8982. |
| [131] | LI HJ, CHANG JL, LIU PF, FU L, DING DW, LU YH. Direct interspecies electron transfer accelerates syntrophic oxidation of butyrate in paddy soil enrichments. Environmental Microbiology, 2015, 17(5): 1533-1547. DOI:10.1111/1462-2920.12576 |
| [132] | van STEENDAM C, SMETS I, SKERLOS S, RASKIN L. Improving anaerobic digestion via direct interspecies electron transfer requires development of suitable characterization methods. Current Opinion in Biotechnology, 2019, 57: 183-190. DOI:10.1016/j.copbio.2019.03.018 |
| [133] | YEE MO, ROTARU AE. Extracellular electron uptake in Methanosarcinales is independent of multiheme c-type cytochromes. Scientific Reports, 2020, 10: 372. DOI:10.1038/s41598-019-57206-z |
| [134] | ROTARU AE, SHRESTHA PM, LIU FH, MARKOVAITE B, CHEN SS, NEVIN KP, LOVLEY DR. Direct interspecies electron transfer between Geobacter metallireducens and Methanosarcina barkeri. Applied and Environmental Microbiology, 2014, 80(15): 4599-4605. DOI:10.1128/AEM.00895-14 |
| [135] | ZHENG SL, ZHANG HX, LI Y, ZHANG H, WANG OM, ZHANG J, LIU FH. Co-occurrence of Methanosarcina mazei and Geobacteraceae in an iron (Ⅲ)-reducing enrichment culture. Frontiers in Microbiology, 2015, 6: 941. |
| [136] | ZHENG SL, LIU FH, WANG BC, ZHANG YC, LOVLEY DR. Methanobacterium capable of direct interspecies electron transfer. Environmental Science & Technology, 2020, 54(23): 15347-15354. |
| [137] | WANG YF, ZHENG AQ, SUN FL, LI M, XU KJ, ZHANG C, LIU SD, XI YJ. Using transcriptome analysis to identify genes involved in switchgrass flower reversion. Frontiers in Plant Science, 2018, 9: 1805. DOI:10.3389/fpls.2018.01805 |
| [138] | LOVLEY DR. Syntrophy goes electric: direct interspecies electron transfer. Annual Review of Microbiology, 2017, 71: 643-664. DOI:10.1146/annurev-micro-030117-020420 |
| [139] | HOLMES DE, SHRESTHA PM, WALKER DJF, DANG Y, NEVIN KP, WOODARD TL, LOVLEY DR. Metatranscriptomic evidence for direct interspecies electron transfer between Geobacter and Methanothrix species in methanogenic rice paddy soils. Applied and Environmental Microbiology, 2017, 83(9): e00223-e00217. |
| [140] | LIU X, ZHAN J, JING XY, ZHOU SG, LOVLEY DR. A pilin chaperone required for the expression of electrically conductive Geobacter sulfurreducens pili. Environmental Microbiology, 2019, 21(7): 2511-2522. DOI:10.1111/1462-2920.14638 |
| [141] | LIU X, ZHUO SY, RENSING C, ZHOU SG. Syntrophic growth with direct interspecies electron transfer between pili-free Geobacter species. The ISME Journal, 2018, 12(9): 2142-2151. DOI:10.1038/s41396-018-0193-y |
| [142] | LIU X, ZHAN J, LIU L, GAN FT, YE J, NEALSON KH, RENSING C, ZHOU SG. In situ spectroelectrochemical characterization reveals cytochrome-mediated electric syntrophy in Geobacter coculture. Environmental Science & Technology, 2021, 55(14): 10142-10151. |
| [143] | YE Y, LIU X, NEALSON KH, RENSING C, QIN SP, ZHOU SG. Dissecting the structural and conductive functions of nanowires in Geobacter sulfurreducens electroactive biofilms. mBio, 2021, 13(1): e0382221. |
| [144] | DENG L, LIU Y, ZHENG D, WANG L, PU XD, LI S, ZHIYONG W, LEI YH, CHEN ZA, LONG Y. Application and development of biogas technology for the treatment of waste in China. Renewable & Sustainable Energy Reviews, 2017, 70: 845-851. |
| [145] | QIAO W, PENG C, WANG W, ZHANG Z. Biogas production from supernatant of hydrothermally treated municipal sludge by upflow anaerobic sludge blanket reactor. Bioresource Technology, 2011, 102(21): 9904-9911. DOI:10.1016/j.biortech.2011.08.037 |
| [146] | WANG T, HUANG Z, RUAN W, ZHAO M, SHAO Y, MIAO H. Insights into sludge granulation during anaerobic treatment of high-strength leachate via a full-scale IC reactor with external circulation system. Journal of Environmental Sciences, 2018, 64: 227-234. DOI:10.1016/j.jes.2017.06.024 |
| [147] | WANG YZ, ZHANG YL, LI JX, LIN JG, ZHANG N, CAO WZ. Biogas energy generated from livestock manure in China: current situation and future trends. Journal of Environmental Management, 2021, 297: 113324. DOI:10.1016/j.jenvman.2021.113324 |
| [148] | YANG H, DENG L, WU J, WANG W, ZHENG D, WANG Z, LIU Y. Intermittent air mixing system for anaerobic digestion of animal wastewater: operating conditions and full-scale validation. Bioresource Technology, 2021, 335: 125304. DOI:10.1016/j.biortech.2021.125304 |
| [149] | DENG L, CAI C, CHEN Z. The treatment of pig slurry by a full-scale anaerobic-adding raw wastewater-intermittent aeration process. Biosystems Engineering, 2007, 98(3): 327-334. DOI:10.1016/j.biosystemseng.2007.08.001 |
| [150] | YANG Z, WANG W, LIU C, ZHANG R, LIU G. Mitigation of ammonia inhibition through bioaugmentation with different microorganisms during anaerobic digestion: selection of strains and reactor performance evaluation. Water Research, 2019, 155: 214-224. DOI:10.1016/j.watres.2019.02.048 |
| [151] | LI Y, YANG G, LI L, SUN Y. Bioaugmentation for overloaded anaerobic digestion recovery with acid-tolerant methanogenic enrichment. Waste Management, 2018, 79: 744-751. DOI:10.1016/j.wasman.2018.08.043 |
| [152] | LI Y, LI L, SUN Y, YUAN Z. Bioaugmentation strategy for enhancing anaerobic digestion of high C/N ratio feedstock with methanogenic enrichment culture. Bioresource Technology, 2018, 261: 188-195. DOI:10.1016/j.biortech.2018.02.069 |
| [153] | HE L, LI L, LI Y, WANG C, SUN Y. Bioaugmentation with methanogenic culture to improve methane production from chicken manure in batch anaerobic digestion. Chemosphere, 2022, 303: 135127. DOI:10.1016/j.chemosphere.2022.135127 |
| [154] | LI Y, WANG C, XU X, SUN Y, XING T. Bioaugmentation with a propionate-degrading methanogenic culture to improve methane production from chicken manure. Bioresource Technology, 2022, 346: 126607. DOI:10.1016/j.biortech.2021.126607 |
| [155] | LI MT, RAO L, WANG L, GOU M, SUN ZY, XIA ZY, SONG WF, TANG YQ. Bioaugmentation with syntrophic volatile fatty acids-oxidizing consortia to alleviate the ammonia inhibition in continuously anaerobic digestion of municipal sludge. Chemosphere, 2022, 288: 132389. DOI:10.1016/j.chemosphere.2021.132389 |
| [156] |
ZHANG X, ZHANG H, CHENG L. Key players involved in methanogenic degradation of organic compounds: progress on the cultivation of syntrophic bacteria. Acta Microbiologica Sinica, 2019, 59(2): 211-223.
(in Chinese) 张雪, 张辉, 承磊. 获取有机物厌氧降解产甲烷过程中关键功能类群: 互营细菌培养物. 微生物学报, 2019, 59(2): 211-223. |
| [157] |
LIU PF, LU YH. A review of syntrophic fatty acids oxidation in anoxic paddy soil. Microbiology China, 2013, 40(1): 109-122.
(in Chinese) 刘鹏飞, 陆雅海. 水稻土中脂肪酸互营氧化的研究进展. 微生物学通报, 2013, 40(1): 109-122. DOI:10.13344/j.microbiol.china.2013.01.005 |
| [158] | SOUSA DZ, SMIDT H, ALVES MM, STAMS AJM. Ecophysiology of syntrophic communities that degrade saturated and unsaturated long-chain fatty acids. FEMS Microbiology Ecology, 2009, 68(3): 257-272. DOI:10.1111/j.1574-6941.2009.00680.x |
| [159] |
DONG XZ. Discussion on the metabolic mechanism of mutual methane production in anaerobic degradation. Microbiology China, 1993, 20(1): 36-42.
(in Chinese) 东秀珠. 厌氧降解中互营产甲烷代谢机制的探讨. 微生物学通报, 1993, 20(1): 36-42. DOI:10.13344/j.microbiol.china.1993.01.012 |
| [160] | MCINERNEY MJ, STRUCHTEMEYER CG, SIEBER J, MOUTTAKI H, STAMS AJM, SCHINK B, ROHLIN L, GUNSALUS RP. Physiology, ecology, phylogeny, and genomics of microorganisms capable of syntrophic metabolism. Annals of the New York Academy of Sciences, 2008, 1125: 58-72. DOI:10.1196/annals.1419.005 |
| [161] | DOLFING J, LARTER SR, HEAD IM. Thermodynamic constraints on methanogenic crude oil biodegradation. The ISME Journal, 2008, 2(4): 442-452. DOI:10.1038/ismej.2007.111 |
| [162] |
WANG LY, MBADINGA SM, LI H, LIU JF, YANG SZ, MOU BZ. Anaerobic biodegradation of petroleum hydrocarbons and enlightenment of the prospects for gasification of residual oil. Microbiology China, 2010, 37(1): 96-102.
(in Chinese) 王立影, Mbadinga Serge Maurice, 李辉, 刘金峰, 杨世忠, 牟伯中. 石油烃的厌氧生物降解对油藏残余油气化开采的启示. 微生物学通报, 2010, 37(1): 96-102. DOI:10.13344/j.microbiol.china.2010.01.020 |
| [163] | GIEG LM, DUNCAN KE, SUFLITA JM. Bioenergy production via microbial conversion of residual oil to natural gas. Applied and Environmental Microbiology, 2008, 74(10): 3022-3029. DOI:10.1128/AEM.00119-08 |
| [164] | CHENG L, DING C, LI Q, HE Q, DAI LR, ZHANG H. DNA-SIP reveals that Syntrophaceae play an important role in methanogenic hexadecane degradation. PLoS One, 2013, 8(7): e66784. DOI:10.1371/journal.pone.0066784 |
| [165] | YE J, YU J, ZHANG Y, CHEN M, LIU X, ZHOU S, HE Z. Light-driven carbon dioxide reduction to methane by Methanosarcina barkeri-CdS biohybrid. Applied Catalysis B: Environmental, 2019, 257: 117916. DOI:10.1016/j.apcatb.2019.117916 |
| [166] | WANG C, YU J, REN GP, HU AD, LIU X, CHEN YP, YE J, ZHOU SG, HE Z. Self-replicating biophotoelectrochemistry system for sustainable CO methanation. Environmental Science & Technology, 2022, 56(7): 4587-4596. |
| [167] | YE J, WANG C, GAO C, FU T, YANG CH, REN GP, LÜ J, ZHOU SG, XIONG YJ. Solar-driven methanogenesis with ultrahigh selectivity by turning down H2 production at biotic-abiotic interface. Nature Communications, 2022, 13: 6612. DOI:10.1038/s41467-022-34423-1 |
| [168] | HUANG LY, LIU X, ZHANG ZS, YE J, RENSING C, ZHOU SG, NEALSON KH. Light-driven carbon dioxide reduction to methane by Methanosarcina barkeri in an electric syntrophic coculture. The ISME Journal, 2022, 16(2): 370-377. DOI:10.1038/s41396-021-01078-7 |
| [169] | THEVASUNDARAM K, GALLAGHER JJ, CHERNG F, CHANG MCY. Engineering nonphotosynthetic carbon fixation for production of bioplastics by methanogenic archaea. Proceedings of the National Academy of Sciences of the United States of America, 2022, 119(23): e2118638119. DOI:10.1073/pnas.2118638119 |