低氧生境中好氧甲烷氧化菌的缺氧耐受机理及种群结构研究进展

甲烷生物氧化在全球大气甲烷平衡和温室气体的控制中起着重要作用.氧气是甲烷生物氧化过程中的重要影响因素之一.生境中氧浓度不仅影响好氧甲烷氧化菌的种群结构、活性及甲烷碳的分配,而且好氧甲烷氧化菌在不同氧浓度下具有不同的代谢途径.理解低氧生境中好氧甲烷氧化菌的缺氧耐受机理和甲烷生物氧化过程,对甲烷驱动型生态系统的碳循环和生物多样性有着重要意义.本文以好氧甲烷氧化菌为对象,综述了低氧生境中好氧甲烷氧化菌的活性及其种群结构、好氧甲烷氧化菌的缺氧耐受机理以及低氧生境中甲烷氧化菌与非甲烷氧化菌的关系,并对今后的研究方向进行了展望.     

兼性甲烷氧化菌的发现历程

兼性甲烷氧化菌在新陈代谢上具有独一无二的特性:它们能够利用甲烷或一些含碳碳键的有机物作为唯一碳源和能源.甲基细胞菌属(Methylocella)、甲基孢囊菌属(Methylocystis)和甲基帽菌属(Methylocapsa)的一些菌株已经被确定为兼性甲烷氧化菌.它们都属于a-变形菌纲,能够像利用甲烷一样在大分子有机酸或乙醇里生长.本文全面系统地总结了兼性甲烷氧化菌的研究发展历史,推断出兼性甲烷氧化菌易在酸性环境富集生长;介绍了与之有相近功能的兼性甲烷氧化生物;浅析了其对多碳化合物的代谢机理;最后讨论了兼性甲烷氧化菌研究的现存问题和工程应用前景.     

甲烷氧化菌及其在环境治理中的应用

甲烷的生物氧化包括好氧氧化和厌氧氧化两种,分别由好氧甲烷氧化菌和厌氧甲烷氧化菌完成.由于该过程是减少自然环境中温室气体甲烷排放的重要途径,越来越受到各国学者的重视.本文主要对当前甲烷氧化菌的研究现状进行了综述,对好氧甲烷氧化菌的种类、参与氧化甲烷的关键酶,厌氧甲烷氧化菌的种类、参与的微生物菌种以及氧化机理进行了论述,并对这两类微生物在温室气体减排、污染物治理、废水生物脱氮、硫及金属元素回收等方面的应用现状及前景进行了分析.     

甲烷氧化过程中铜的作用研究进展

甲烷生物氧化在全球甲烷平衡和温室效应控制中扮演着重要的角色,而铜是甲烷生物氧化过程中的重要影响因子.一方面,铜是调控不同类型甲烷单加氧酶表达的主要影响因子,是组成颗粒性甲烷单加氧酶的必需金属元素;另一方面,在自然环境体系中,铜含量及其形态的变化对甲烷氧化菌的分布、代谢甲烷和非甲烷类有机化合物的能力以及甲烷氧化菌的特异性铜捕获系统也会产生较大影响.准确把握铜在甲烷生物氧化过程中发挥的作用将有助于全面了解甲烷生物氧化过程,进而更好地指导甲烷氧化微生物在温室气体减排及非甲烷有机物污染修复中的应用.本文主要从铜的角度,概述了铜对甲烷氧化菌的分布和活性的影响,介绍了铜在调控甲烷单加氧酶的表达和活性以及调节甲烷氧化菌铜捕获系统方面的作用,并展望了其研究方向.     

好氧甲烷氧化菌生理生态特征及其在自然湿地中的群落多样性研究进展

甲烷氧化菌是一类可以利用甲烷作为唯一碳源和能源的细菌,在全球变化和整个生态系统碳循环过程中起着重要的作用。近年来,对甲烷氧化菌的生理生态特征及其在自然湿地中的群落多样性研究取得了较大进展。在分类方面,疣微菌门、NC10门及两个丝状菌属甲烷氧化菌的发现使其分类体系得到了进一步的完善;在单加氧酶方面,发现甲烷氧化菌可以利用pM MO和sM MO两种酶进行氧化甲烷的第一步反应,Ⅱ型甲烷氧化菌中pM MO2的发现证实甲烷氧化菌可以利用这种酶氧化低浓度的甲烷;在底物利用方面,已经发现了越来越多的兼性营养型甲烷氧化菌,证实它们可以利用的底物比之前认为的更广泛,其中包括乙酸等含有碳碳键的化合物;在生存环境方面,能在不同温度、酸度和盐度的环境中生存的甲烷氧化菌不断被分离出来。全球自然湿地甲烷氧化菌群落多样性的研究目前主要集中在北半球高纬度的酸性泥炭湿地,Ⅱ型甲烷氧化菌Methylocystis、Methylocella和Methylocapsa是这类湿地主要的甲烷氧化菌类群,尤其以Methylocystis类群最为广泛,而Ⅰ型甲烷氧化菌尤其是Methylobacter在北极寒冷湿地中占优势。随着高通量测序时代的到来和新的分离技术的发展,对甲烷氧化菌的现有认识将面临更多的挑战和发展。     

生物分子机器——甲烷单加氧酶的研究进展

甲烷氧化菌中的甲烷单加氧酶能够在生理条件下选择性地以甲烷和氧气为底物生成甲醇,麻省理工学院的Lippard教授称它为"神奇的生物分子机器"。本文重点对生物分子机器甲烷单加氧酶的结构、编码基因及调控机制、催化反应机理等进行了综述,此外也简要介绍了甲烷单加氧酶的产生菌甲烷氧化菌的研究历史及分类。生物分子机器甲烷单加氧酶可催化甲烷氧化成甲醇,不仅为甲醇的生产提供了一种新颖的生产方法,而且对生物分子机器的设计也有借鉴意义。     

陆地生态系统甲烷产生和氧化过程的微生物机理

陆地生态系统存在许多常年性或季节性缺氧环境,如:湿地、水稻土、湖泊沉积物、动物瘤胃、垃圾填埋场和厌氧生物反应器等。每年有大量有机物质进入这些环境,在缺氧条件下发生厌氧分解。甲烷是有机质厌氧分解的最终产物。产生的甲烷气体可通过缺氧-有氧界面释放到大气,产生温室效应,是重要的温室气体。产甲烷过程是缺氧环境中有机质分解的核心环节,而甲烷氧化是缺氧-有氧界面的重要微生物过程。甲烷的产生和氧化过程共同调控大气甲烷浓度,是全球碳循环不可分割的组成部分。对陆地生态系统甲烷产生和氧化过程的微生物机理研究进展进行了概要回顾和综述。主要内容包括:新型产甲烷古菌即第六和第七目产甲烷古菌和嗜冷嗜酸产甲烷古菌的发现;短链脂肪酸中间产物互营氧化过程与直接种间电子传递机制;新型甲烷氧化菌包括厌氧甲烷氧化菌和疣微菌属好氧甲烷氧化菌的发现;甲烷氧化菌生理生态与环境适应的新机制。这些研究进展显著拓展了人们对陆地生态系统甲烷产生和氧化机理的认识和理解。随着新一代土壤微生物研究技术的发展与应用,甲烷产生和氧化微生物研究领域将面临更多机遇和挑战,对未来发展趋势做了展望。     

土壤CH_4氧化与土壤甲烷营养菌及主要研究方法

甲烷营养菌(methanotrophs)是一类以CH_4为唯一碳源和能源的细菌,广泛分布在水稻土、森林土、苔原土、泥炭地、海洋与湖泊底泥、堆肥、垃圾填埋场及地下水等环境中,并作为大气甲烷(CH_4)唯一的生物汇(库),在全球温室效应研究中备受关注.目前,关于土壤甲烷营养菌的研究主要包括菌株的多样性、生态分布以及环境因素对微生物氧化CH_4过程的影响.本文从甲烷营养菌的分类入手,概述稻田土壤CH_4的氧化与释放、旱地土壤CH_4的氧化以及影响土壤CH_4氧化的因素等方面的研究进展,同时介绍了土壤甲烷营养菌研究领域的几种主要的分子研究技术,以期为甲烷营养菌相关的研究提供参考.     

酸微菌纲(Acidimicrobiia)的研究概况

酸微菌是酸微菌纲(Acidimicrobiia)下所有菌的统称,广泛存在于酸性矿废水和海洋、湖泊、土壤、沙漠等环境,因其难培养、特殊的生理特性而受到特别的关注。酸微菌在酸性、中性和弱碱性环境中均有分布,一部分种属嗜酸、中度嗜热、可进行Fe2+氧化和Fe3+还原反应,具有矿石氧化和合成新型活性物质的能力,在生物浸矿与化学合成有潜在的应用价值;一部分种属存在于中性或弱碱性的土壤、沙漠和水体中,是该类环境中放线菌的优势种类。本文概述了酸微菌纲的建立和发展、酸微菌的系统发育、生物多样性与地理分布、主要生理特性、代谢途径、基因组研究等情况,并对酸微菌的应用前景和未来研究方向进行展望。     

好氧甲烷氧化菌及其工程应用进展

好氧甲烷氧化菌能以甲烷作为碳源和能源,对全球甲烷消除的贡献率高达10%–20%,还能有效地合成有价值的甲烷来源生物产品。文中介绍了好氧甲烷氧化菌的甲烷氧化代谢机理,总结了好氧甲烷氧化菌在填埋场甲烷减排、煤矿通风气治理、合成生物产品、油气藏勘探等领域的实际应用功效和研究热点,即污染物去除和产品合成效率的影响因素。基于对甲烷氧化菌规模化培养方法的研究,本文认为加强培养过程中代谢产物对甲烷氧化菌活性和种群结构影响的研究,以及开发经济高效的替代培养基和培养技术的研究将有利于好氧甲烷氧化菌生物技术的应用推广。     

Group-specific quantification of methanotrophs in landfill gas-purged laboratory biofilters by tyramide signal amplification-fluorescence in situ hybridization

The aim of this study was to quantitatively analyse methanotrophs in two laboratory landfill biofilters at different biofilter depths and at temperatures which mimicked the boreal climatic conditions. Both biofilters were dominated by type I methanotrophs. The biofilter depth profiles showed that type I methanotrophs occurred in the upper layer, where relatively high O(2) and low CH(4) concentrations were present, whereas type II methanotrophs were mostly distributed in the zone with high CH(4) and low O(2) concentrations. The number of type I methanotrophic cells declined when the temperature was raised from 15 degrees C to 23 degrees C, but increased when lowered to 5 degrees C. A slight decrease in type II methanotrophs was also observed when the temperature was raised from 15 degrees C to 23 degrees C, whereas cell numbers remained constant when lowered to 5 degrees C. The results indicated that low temperature conditions favored both type I and type II methanotrophs in the biofilters.     

Group-specific 16S rRNA targeted probes for the detection of type I and type II methanotrophs by fluorescence in situ hybridisation

The study of methane-oxidising bacteria (methanotrophs) is of special interest, because of their role in the natural reduction of methane emissions from many different sources. Therefore new probes were developed to detect specifically either type I (Methylococcaceae) or type II methanotrophs (Methylocystaceae). The probes have shown high specificity in fluorescence in situ hybridisations (FISH), as demonstrated by parallel hybridisation of target and reference strains as well as sequence data analysis. With these probes, methanotrophs were detected in soil and root samples from rice microcosms, demonstrating their applicability even in a complex environmental matrix.     

Biology of extremophilic and extremotolerant methanotrophs

This review summarizes recent findings on the biology of obligate methanotrophic bacteria living in various extreme environments. By using molecular ecology techniques, it has become clear that obligate methanotrophs are ubiquitous in nature and well adapted to high or low temperature, pH and salinity. The isolation and characterization of pure cultures has led to the discovery of several new genera and species of extremophilic/tolerant methanotrophs. Their major physiological role is participation in the methane cycle and supplying C(1) intermediates and various metabolites to other members of microbial communities in extreme ecosystems. To survive under extreme conditions, methanotrophs have developed diverse structure-function adaptive mechanisms including cell-surface layer formation, changes in cellular phospholipid composition and de novo synthesis of organic osmolytes such as ectoine, 5-oxoproline and sucrose. However, despite the above advances, basic knowledge of other stress protectants, as well as bioenergetic and genetic aspects of methanotroph adaptation, is still lacking. This information is necessary for better understanding the molecular mechanisms underlying the versatility of methanotrophs and for the development of novel biotechnological processes.     

Methane-oxidizing bacteria in a California upland grassland soil: diversity and response to simulated global change

We investigated the diversity of methane-oxidizing bacteria (i.e., methanotrophs) in an annual upland grassland in northern California, using comparative sequence analysis of the pmoA gene. In addition to identifying type II methanotrophs commonly found in soils, we discovered three novel pmoA lineages for which no cultivated members have been previously reported. These novel pmoA clades clustered together either with clone sequences related to "RA 14" or "WB5FH-A," which both represent clusters of environmentally retrieved sequences of putative atmospheric methane oxidizers. Conservation of amino acid residues and rates of nonsynonymous versus synonymous nucleotide substitution in these novel lineages suggests that the pmoA genes in these clades code for functionally active methane monooxygenases. The novel clades responded to simulated global changes differently than the type II methanotrophs. We observed that the relative abundance of type II methanotrophs declined in response to increased precipitation and increased atmospheric temperature, with a significant antagonistic interaction between these factors such that the effect of both together was less than that expected from their individual effects. Two of the novel clades were not observed to respond significantly to these environmental changes, while one of the novel clades had an opposite response, increasing in relative abundance in response to increased precipitation and atmospheric temperature, with a significant antagonistic interaction between these factors.     

Fate of 2,2,2-trichloroacetaldehyde (chloral hydrate) produced during trichloroethylene oxidation by methanotrophs.

Four different methanotrophs expressing soluble methane monooxygenase produced 2,2,2-trichloroacetaldehyde, or chloral hydrate, a controlled substance, during the oxidation of trichloroethylene. Chloral hydrate concentrations decreased in these cultures between 1 h and 24 h of incubation. Chloral hydrate was shown to be biologically transformed to trichloroethanol and trichloroacetic acid by Methylosinus trichosporium OB3b. At elevated pH and temperature, chloral hydrate readily decomposed and chloroform and formic acid were detected as products.     

Fate of 2,2,2-trichloroacetaldehyde (chloral hydrate) produced during trichloroethylene oxidation by methanotrophs.

Four different methanotrophs expressing soluble methane monooxygenase produced 2,2,2-trichloroacetaldehyde, or chloral hydrate, a controlled substance, during the oxidation of trichloroethylene. Chloral hydrate concentrations decreased in these cultures between 1 h and 24 h of incubation. Chloral hydrate was shown to be biologically transformed to trichloroethanol and trichloroacetic acid by Methylosinus trichosporium OB3b. At elevated pH and temperature, chloral hydrate readily decomposed and chloroform and formic acid were detected as products.     

Variation of salinity and nitrogen concentration affects the pentacyclic triterpenoid inventory of the haloalkaliphilic aerobic methanotrophic bacterium Methylotuvimicrobium alcaliphilum

Extremophiles - The occurrence and activity of aerobic methanotrophs are influenced by environmental conditions, including pH, temperature, salinity, methane and oxygen concentrations, and nutrient...     

So close,so different: geothermal flux shapes divergent soil microbial communities at neighbouring sites

This study is focused on the (micro)biogeochemical features of two close geothermal sites (FAV1 and FAV2), both selected at the main exhalative area of Pantelleria Island, Italy. A previous biogeochemical survey revealed high CH₄ consumption and the presence of a diverse community of methanotrophs at FAV2 site, whereas the close site FAV1 was apparently devoid of methanotrophs and recorded no CH₄ consumption. Next‐Generation Sequencing (NGS) techniques were applied to describe the bacterial and archaeal communities which have been linked to the physicochemical conditions and the geothermal sources of energy available at the two sites. Both sites are dominated by Bacteria and host a negligible component of ammonia‐oxidizing Archaea (phylum Thaumarchaeota). The FAV2 bacterial community is characterized by an extraordinary diversity of methanotrophs, with 40% of the sequences assigned to Methylocaldum, Methylobacter (Gammaproteobacteria) and Bejerickia (Alphaproteobacteria); conversely, a community of thermo‐acidophilic chemolithotrophs (Acidithiobacillus, Nitrosococcus) or putative chemolithotrophs (Ktedonobacter) dominates the FAV1 community, in the absence of methanotrophs. Since physical andchemical factors of FAV1, such as temperature and pH, cannot be considered limiting for methanotrophy, it is hypothesized that the main limiting factor for methanotrophs could be high NH₄⁺ concentration. At the same time, abundant availability of NH₄⁺ and other high energy electron donors and acceptors determined by the hydrothermal flux in this site create more energetically favourable conditions for chemolithotrophs that outcompete methanotrophs in non‐nitrogen‐limited soils.     

Trichloroethylene biodegradation by mesophilic and psychrophilic ammonia oxidizers and methanotrophs in groundwater microcosms.

This study investigated the efficiency of methane and ammonium for stimulating trichloroethylene (TCE) biodegradation in groundwater microcosms (flasks and batch exchange columns) at a psychrophilic temperature (12 degrees C) typical of shallow aquifers in the northern United States or a mesophilic temperature (24 degrees C) representative of most laboratory experiments. After 140 days, TCE biodegradation rates by ammonia oxidizers and methanotrophs in mesophilic flask microcosms were similar (8 to 10 nmol day-1), but [14C]TCE mineralization (biodegradation to 14CO2) by ammonia oxidizers was significantly greater than that by methanotrophs (63 versus 53%). Under psychrophilic conditions, [14C]TCE mineralization in flask systems by ammonia oxidizers and methanotrophs was reduced to 12 and 5%, respectively. In mesophilic batch exchange columns, average TCE biodegradation rates for methanotrophs (900 nmol liter-1 day-1) were not significantly different from those of ammonia oxidizers (775 nmol liter-1 day-1). Psychrophilic TCE biodegradation rates in the columns were similar with both biostimulants and averaged 145 nmol liter-1 day-1. Methanotroph biostimulation was most adversely affected by low temperatures. At 12 degrees C, the biodegradation efficiencies (TCE degradation normalized to microbial activity) of methanotrophs and ammonia oxidizers decreased by factors of 2.6 and 1.6, respectively, relative to their biodegradation efficiencies at 24 degrees C. Collectively, these experiments demonstrated that in situ bioremediation of TCE is feasible at the psychrophilic temperatures common in surficial aquifers in the northern United States and that for such applications biostimulation of ammonia oxidizers could be more effective than has been previously reported.