地下水脱卤过程中的微生物种间代谢互作：提高原位氯代烯烃厌氧脱氯效能的有效途径

有机卤呼吸细菌(organohalide-respiring bacteria, OHRB)在氯代烯烃污染地下水的原位生物修复中扮演着关键性的角色,提高其丰度及活性对氯代烯烃的完全去除具有重要意义。在实际环境中,有机卤呼吸细菌往往与多种微生物共存,微生物种间代谢互作现象十分普遍,有机污染物的完全无害化往往需要通过微生物菌群的协同代谢作用来实现。因此,本文围绕微生物种间代谢互作进行综述,对目前获得的脱氯微生物菌种资源及脱氯机理进行了回顾,重点阐述了专性OHRB、非专性OHRB和非OHRB的种间代谢互作行为及机制,并提出以种间代谢互作为指导进行合成微生物群落的构建来有效提高氯代烯烃厌氧生物降解效率,为实现环境氯代烯烃类有机污染物的快速、彻底无害化提供理论指导。     

环境因子对厌氧微生物脱卤的影响研究进展

有机卤代物在工农业生产中的广泛应用及不合理处置与排放导致其成为地下环境中普遍存在的一类污染物,严重威胁地下生态系统功能、饮用水安全和人类健康。有机卤呼吸细菌在有机卤污染场地的原位生物修复中起到了至关重要的作用。本文简要概述了影响和制约有机卤呼吸微生物生长代谢及脱卤活性的一些关键环境因子,如pH、温度、盐度、电子供受体和氧气等,并且对有机卤呼吸细菌未来的研究方向提出展望,以期为污染场地原位生物修复工程的有效实施提供理论与技术参考。     

微生物厌氧呼吸与有机污染水体沉积物修复

水体沉积物有机污染是当前全球关注的重要环境问题。微生物具有呼吸和代谢多样性,能以多种污染物作为厌氧呼吸的电子供体或受体,与周围环境中的生物和非生物因素组成代谢网络耦合有机污染物降解转化,是有机污染水体沉积物修复的重要驱动者。本文重点综述了微生物厌氧呼吸、电子传递网络及其对有机污染水体沉积物的修复机制研究进展,并对有机污染水体沉积物微生物修复理论和技术研究的问题和挑战进行了探讨。     

环境中污染物降解基因的水平转移(HGT)及其在生物修复中的作用

水平基因转移是不同于垂直基因转移的遗传物质的交流方式.在污染环境这一特异生态环境中,降解基因的水平转移有着独特的功能与作用.研究环境中污染物降解基因在微生物间的水平转移,更深入地了解微生物种群适应污染环境的机理,对于评价污染物的环境毒理、生物可降解性以及污染环境的可修复潜力具有重要参考价值.在污染物生物修复实践中,可以通过调控降解基因的水平转移,增强污染环境中微生物的降解能力,更有效地发挥生物修复作用.文章将对环境中细菌间基因交流的机制,污染物降解基因的水平转移对微生物适应污染环境的机理、水平基因转移对代谢途径的进化及其对污染物生物修复作用的影响等方面的研究进展做一综述.     

1,2,3-三氯丙烷降解机制与污染场地修复技术研究进展

1,2,3-三氯丙烷(1,2,3-trichloropropane,1,2,3-TCP)是一种人工合成的脂肪族氯代烃,在工、农业生产中得到广泛应用。1,2,3-TCP作为环氧氯丙烷工业生产的中间产物,可作为前体物质用于生产土壤熏蒸剂、有机溶剂等。因其环境持久性、迁移性和生态毒性,国内外机构逐渐开始关注该有机氯污染物的环境归趋、生态健康风险和环境管控。当前,1,2,3-TCP污染物的降解与场地修复仍然是研究热点,但是对于1,2,3-TCP降解转化机制尚缺乏深入研究与总结。鉴于此,文中在讨论1,2,3-TCP的来源、环境污染、生态效应及物理化学降解方法与技术等的基础上,进一步综述了1,2,3-TCP的微生物降解与修复机制(如好氧共代谢降解、厌氧降解等);重点讨论了地下水等厌氧环境中1,2,3-TCP的厌氧微生物降解转化途径与机制,并从热力学角度论证了厌氧条件下1,2,3-TCP作为电子受体被有机卤呼吸微生物利用并降解的可行性;最后,对1,2,3-TCP污染场地原位生物修复进行了总结并对未来研究发展方向进行了展望。     

植物根系分泌物对土壤污染修复的作用及影响机理

生物修复是一种经济环保的土壤修复技术。根系分泌物是利用生物修复污染土壤过程中的关键物质,也是植物与土壤微生物进行物质交换和信息传递的重要载体,在植物响应污染物胁迫中扮演重要角色。研究植物根系分泌物对土壤污染修复的作用和影响机理,是深入理解植物和微生物环境适应机制的重要途径,对促进生物修复污染土壤有重要指导意义。从污染物胁迫对根系分泌物的影响、根系分泌物对土壤污染物环境行为的影响、根系分泌物在调控污染土壤中根际微生物群落结构和多样性中发挥的作用等几个方面综述了根系分泌物对土壤污染修复的影响及内在机制。研究结果表明,根系分泌物在降低重金属对植物的毒性、加速有机污染物降解等方面有非常重要的作用。根系分泌物对土壤微生物的丰度和多样性均有显著影响,其与根际微生物互作在土壤污染物的消减中发挥了重要的调控作用。在此基础上,提出了以往研究中的不足,并对污染物胁迫下根系分泌物未来研究的方向和趋势进行了展望。     

土壤重金属和有机污染物的微生物修复:生物强化和生物刺激

生物强化和生物刺激等绿色技术以其经济有效、生态友好的特性,已逐渐成为治理土壤重金属和有机污染的利器。多种细菌、真菌及混合菌群可与物理化学修复手段灵活组合,针对性开展土壤有机污染、重金属污染及复合污染修复。总结近5年代表性研究结果,讨论处理菌株的多来源筛选,其转化/降解不同类型污染物的潜力,着重其在多尺度土壤治理案例中的应用,包括实验室、温室和场地条件下的修复表现。微生物修复的复杂性不仅由于菌的生理和代谢特性差异,还表现在影响因素众多,包括非生物因素,如p H、温度、土壤类型、污染物浓度、水和有机质含量,外加碳源和氮源等生物因素,如接种量,外加菌株和原地土著菌互作,接种物存活等。指出今后联合修复思路和加强分子方法应用的研究方向。     

基于多Agent仿真解析处理剩余污泥的微生物电解池种群互作关系

【背景】微生物电化学系统耦合了电化学反应和厌氧消化过程,在处理剩余污泥同时实现能源回收,成为具有应用前景的技术之一。揭示电活性生物膜和活性污泥种群互作机制,有助于进一步调控和强化系统性能。高通量核酸测序技术研究微生物群落具有投入大、耗时长和不可预测的缺点,开展微生物群落动态仿真可以更有效地预测群落结构与功能。【目的】研究厌氧消化和生物电化学系统的微生物种间热力学与动力学的演化规律。在考虑电子供体、电子受体、温度、pH值等生态条件下,分析底物的电子流向及微生物群落结构的动态变化。【方法】通过对剩余污泥处理的微生物电解池(Microbial electrolytic cell,MEC)建立一个多Agent仿真(Multi-agent-based simulation,MAS)模型,评估MEC对底物氧化电子转移的能量效率和传质效率,模拟微生物群落结构实时变化,同时耦合动力学和热力学分析;揭示影响MES运行的电子流向决定性因素及相应的微生物种群,为复杂污染物生物处理系统中种间互作和动力学研究提供基础依据。【结果】通过MAS模拟,确定MEC污泥处理工艺的最佳能量传递效率与传质效率为η=0.2,ε=0.5,MAS结合热力学与动力学参数模拟微生物的群落动态与实验组有较高的吻合性。在长期的运行中,微生物电化学系统中丙酮酸没有积累。【结论】证实了MAS结合热力学与动力学参数可以预测微生物的群落动态,并进行实时监测。研究表明多Agent仿真为微生物群落结构动态变化提供了一种新的研究方法,该方法与高通量核酸测序技术进行校验和联用,为人工和自然生态系统中微生物种群预测与评估研究提供一个新的手段。     

六氯-1,3-丁二烯的微生物降解研究进展

六氯-1,3-丁二烯(hexachlorobutadiene,HCBD)是一种有毒有害的脂肪族氯代烃,曾经作为杀虫剂、除草剂、变压器油和传热流体等化学工业产品的重要成分被广泛应用于生产生活。HCBD因满足《关于持久性有机污染物的斯德哥尔摩公约》中风险筛选标准(如毒性、持久性、远距离环境迁移和生物累积性等),缔约方于2015年第七次会议中将其增列为持久性有机污染物,2017年又将其列入该公约的附件Ｃ以控制其环境排放量。目前关于HCBD的环境归趋仍是研究热点,但是对于HCBD的微生物降解转化机制尚缺乏深入研究。鉴于此,本文重点回顾并讨论了地下水、底泥等厌氧环境中已报道的HCBD微生物降解转化途径、速率及机制,并从热力学角度阐述HCBD及其降解产物作为电子受体通过还原性脱氯反应被厌氧脱卤微生物代谢转化的可行性。最后,本文根据现有研究结果,提出微生物厌氧降解HCBD的研究展望,包括多组学技术解析HCBD降解功能菌群结构和潜在互作机制、HCBD厌氧降解微生物的分离与纯化,以及HCBD厌氧降解菌剂的开发与污染场地原位生物修复应用等。     

水体沉积物中微生物厌氧呼吸耦合多环芳烃降解的研究进展

多环芳烃(Polycyclic aromatic hydrocarbons,PAHs)是一种具有致癌、致畸、致突变的持久性有机污染物。本文在分析国内外主要水体沉积物中PAHs污染状况的基础上,综述了近几年有关厌氧水体沉积物中微生物以硝酸盐、Fe(III)以及硫酸盐为电子受体进行呼吸耦合PAHs降解的研究概况。此外,还总结了基于微生物的PAHs降解基因组、蛋白质组、代谢组以及菌群水平上互作网络的研究进展,以期为进一步加速PAHs污染水体沉积物原位生物修复提供科学理论参考。     

Fitness and stability of obligate cross-feeding interactions that emerge upon gene loss in bacteria

Cross-feeding interactions, in which bacterial cells exchange costly metabolites to the benefit of both interacting partners, are very common in the microbial world. However, it generally remains unclear what maintains this type of interaction in the presence of non-cooperating types. We investigate this problem using synthetic cross-feeding interactions: by simply deleting two metabolic genes from the genome of Escherichia coli, we generated genotypes that require amino acids to grow and release other amino acids into the environment. Surprisingly, in a vast majority of cases, cocultures of two cross-feeding strains showed an increased Darwinian fitness (that is, rate of growth) relative to prototrophic wild type cells—even in direct competition. This unexpected growth advantage was due to a division of metabolic labour: the fitness cost of overproducing amino acids was less than the benefit of not having to produce others when they were provided by their partner. Moreover, frequency-dependent selection maintained cross-feeding consortia and limited exploitation by non-cooperating competitors. Together, our synthetic study approach reveals ecological principles that can help explain the widespread occurrence of obligate metabolic cross-feeding interactions in nature.     

代谢互养关系在维持微生物物种多样性中的作用

互养关系（cross-feeding）是微生物物种之间普遍存在的一种相互关系，其中物种利用环境中其他成员的代谢产物以促进自身生长的情形称为代谢互养关系，这种关系对物种间的竞争结果往往有很大影响，甚至会改变种群结构。为了研究代谢互养关系在维持微生物物种多样性中的作用，构建包含不同代谢互养关系的资源竞争模型，这些模型既体现了微生物物种竞争资源时种群密度及资源量的动态，也展示了物种利用其他竞争者的代谢资源对自身生存状况的影响。数值模拟结果显示：（1）考虑微生物中不同的代谢互养关系结构：两物种间单向互养、双向互养以及多物种间的互养，不同的互养关系都可以促进竞争物种稳定共存，竞争中处于劣势的物种通过利用其他竞争成员的代谢产物，打破外界资源量对其生长的限制，改变原本消亡的命运；而处于优势的物种则通过利用其他竞争成员的代谢产物，增大种群密度。（2）多物种竞争同一种有限资源时，不是所有物种都能共存，在四物种模拟中，原本处于最劣势的物种灭绝，其余三者共存。物种产生代谢资源对其本身是"不利"的，如果在模拟中物种利用代谢资源的能力相同，那么物种竞争外界资源的劣势就很可能无法被抵消。通过改变资源利用率发现只有互养关系中代谢资源的利用可以弥补劣势种在竞争外界资源时的不足，多物种才可以全部共存。（3）验证数值模拟结果的普遍性，分析参数变化对共存的影响，结果表明代谢互养关系促进的共存对代谢资源相关参数不敏感，参数的改变只影响平衡态时物种的种群密度。所以，代谢互养关系可以促进相互竞争的微生物物种共存，即微生物之间的互养关系很可能是维持物种多样性的一种机制。     

Sulfide alters microbial functional potential in a methane and nitrogen cycling biofilm reactor

Cross-feeding of metabolites between coexisting cells leads to complex and interconnected elemental cycling and microbial interactions. These relationships influence overall community function and can be altered by changes in substrate availability. Here, we used isotopic rate measurements and metagenomic sequencing to study how cross-feeding relationships changed in response to stepwise increases of sulfide concentrations in a membrane-aerated biofilm reactor that was fed with methane and ammonium. Results showed that sulfide: (i) decreased nitrite oxidation rates but increased ammonia oxidation rates; (ii) changed the denitrifying community and increased nitrous oxide production; and (iii) induced dissimilatory nitrite reduction to ammonium (DNRA). We infer that inhibition of nitrite oxidation resulted in higher nitrite availability for DNRA, anammox, and nitrite-dependent anaerobic methane oxidation. In other words, sulfide likely disrupted microbial cross-feeding between AOB and NOB and induced cross-feeding between AOB and nitrite reducing organisms. Furthermore, these cross-feeding relationships were spatially distributed between biofilm and planktonic phases of the reactor. These results indicate that using sulfide as an electron donor will promote N₂O and ammonium production, which is generally not desirable in engineered systems.     

Combinational quorum sensing devices for dynamic control in cross-feeding cocultivation

Quorum sensing (QS) offers cell density dependent dynamic regulations in cell culture through devices such as synchronized lysis circuit (SLC) and metabolic toggle switch (MTS). However, there is still a lack of studies on cocultivation with a combination of different QS-based devices. Taking the production of isopropanol and salidroside as case studies, we have mathematically modeled a comprehensive set of QS-regulated cocultivation schemes and constructed experimental combinations of QS devices, respectively, to evaluate their feasibility and optimality for regulating growth competition and corporative production. Glucose split ratio is proposed for the analysis of competition between cell growth and targeted production. Results show that the combination of different QS devices across multiple members offers a new tool with the potential to effectively coordinate synthetic microbial consortia for achieving high product titer in cross-feeding cocultivation. It is also evident that the performance of such systems is significantly affected by dynamic characteristics of chosen QS devices, carbon source control and the operational settings. This study offers insights for future applications of combinational QS devices in synthetic microbial consortia.     

Microbial Community Response of an Organohalide Respiring Enrichment Culture to Permanganate Oxidation

While in situ chemical oxidation is often used to remediate tetrachloroethene (PCE) contaminated locations, very little is known about its influence on microbial composition and organohalide respiration (OHR) activity. Here, we investigate the impact of oxidation with permanganate on OHR rates, the abundance of organohalide respiring bacteria (OHRB) and reductive dehalogenase (rdh) genes using quantitative PCR, and microbial community composition through sequencing of 16S rRNA genes. A PCE degrading enrichment was repeatedly treated with low (25 μmol), medium (50 μmol), or high (100 μmol) permanganate doses, or no oxidant treatment (biotic control). Low and medium treatments led to higher OHR rates and enrichment of several OHRB and rdh genes, as compared to the biotic control. Improved degradation rates can be attributed to enrichment of (1) OHRB able to also utilize Mn oxides as a terminal electron acceptor and (2) non-dechlorinating community members of the Clostridiales and Deltaproteobacteria possibly supporting OHRB by providing essential co-factors. In contrast, high permanganate treatment disrupted dechlorination beyond cis-dichloroethene and caused at least a 2–4 orders of magnitude reduction in the abundance of all measured OHRB and rdh genes, as compared to the biotic control. High permanganate treatments resulted in a notably divergent microbial community, with increased abundances of organisms affiliated with Campylobacterales and Oceanospirillales capable of dissimilatory Mn reduction, and decreased abundance of presumed supporters of OHRB. Although OTUs classified within the OHR-supportive order Clostridiales and OHRB increased in abundance over the course of 213 days following the final 100 μmol permanganate treatment, only limited regeneration of PCE dechlorination was observed in one of three microcosms, suggesting strong chemical oxidation treatments can irreversibly disrupt OHR. Overall, this detailed investigation into dose-dependent changes of microbial composition and activity due to permanganate treatment provides insight into the mechanisms of OHR stimulation or disruption upon chemical oxidation.     

The role of competition versus cooperation in microbial community coalescence

New microbial communities often arise through the mixing of two or more separately assembled parent communities, a phenomenon that has been termed “community coalescence”. Understanding how the interaction structures of complex parent communities determine the outcomes of coalescence events is an important challenge. While recent work has begun to elucidate the role of competition in coalescence, that of cooperation, a key interaction type commonly seen in microbial communities, is still largely unknown. Here, using a general consumer-resource model, we study the combined effects of competitive and cooperative interactions on the outcomes of coalescence events. To do so, we simulate coalescence events between pairs of communities with different degrees of competition for shared carbon resources and cooperation through cross-feeding on leaked metabolic by-products (facilitation). We also study how structural and functional properties of post-coalescence communities evolve when they are subjected to repeated coalescence events. We find that in coalescence events, the less competitive and more cooperative parent communities contribute a higher proportion of species to the new community because of their superior ability to deplete resources and resist invasions. Consequently, when a community is subjected to repeated coalescence events, it gradually evolves towards being less competitive and more cooperative, as well as more speciose, robust and efficient in resource use. Encounters between microbial communities are becoming increasingly frequent as a result of anthropogenic environmental change, and there is great interest in how the coalescence of microbial communities affects environmental and human health. Our study provides new insights into the mechanisms behind microbial community coalescence, and a framework to predict outcomes based on the interaction structures of parent communities.     

Evolution of cooperative cross-feeding could be less challenging than originally thought

The act of cross-feeding whereby unrelated species exchange nutrients is a common feature of microbial interactions and could be considered a form of reciprocal altruism or reciprocal cooperation. Past theoretical work suggests that the evolution of cooperative cross-feeding in nature may be more challenging than for other types of cooperation. Here we re-evaluate a mathematical model used previously to study persistence of cross-feeding and conclude that the maintenance of cross-feeding interactions could be favoured for a larger parameter ranges than formerly observed. Strikingly, we also find that large populations of cross-feeders are not necessarily vulnerable to extinction from an initially small number of cheats who receive the benefit of cross-feeding but do not reciprocate in this cooperative interaction. This could explain the widespread cooperative cross-feeding observed in natural populations.     

Thermodynamic constraints on the assembly and diversity of microbial ecosystems are different near to and far from equilibrium

Non-equilibrium thermodynamics has long been an area of substantial interest to ecologists because most fundamental biological processes, such as protein synthesis and respiration, are inherently energy-consuming. However, most of this interest has focused on developing coarse ecosystem-level maximisation principles, providing little insight into underlying mechanisms that lead to such emergent constraints. Microbial communities are a natural system to decipher this mechanistic basis because their interactions in the form of substrate consumption, metabolite production, and cross-feeding can be described explicitly in thermodynamic terms. Previous work has considered how thermodynamic constraints impact competition between pairs of species, but restrained from analysing how this manifests in complex dynamical systems. To address this gap, we develop a thermodynamic microbial community model with fully reversible reaction kinetics, which allows direct consideration of free-energy dissipation. This also allows species to interact via products rather than just substrates, increasing the dynamical complexity, and allowing a more nuanced classification of interaction types to emerge. Using this model, we find that community diversity increases with substrate lability, because greater free-energy availability allows for faster generation of niches. Thus, more niches are generated in the time frame of community establishment, leading to higher final species diversity. We also find that allowing species to make use of near-to-equilibrium reactions increases diversity in a low free-energy regime. In such a regime, two new thermodynamic interaction types that we identify here reach comparable strengths to the conventional (competition and facilitation) types, emphasising the key role that thermodynamics plays in community dynamics. Our results suggest that accounting for realistic thermodynamic constraints is vital for understanding the dynamics of real-world microbial communities.