Resilience vs. historical contingency in microbial responses to environmental change

How soil processes such as carbon cycling will respond to future climate change depends on the responses of complex microbial communities, but most ecosystem models assume that microbial functional responses are resilient and can be predicted from simple parameters such as biomass and temperature. Here, we consider how historical contingencies might alter those responses because function depends on prior conditions or biota. Functional resilience can be driven by physiological, community or adaptive shifts; historical contingencies can result from the influence of historical environments or a combination of priority effects and biotic resistance. By modelling microbial population responses to environmental change, we demonstrate that historical environments can constrain soil function with the degree of constraint depending on the magnitude of change in the context of the prior environment. For example microbial assemblages from more constant environments were more sensitive to change leading to poorer functional acclimatisation compared to microbial assemblages from more fluctuating environments. Such historical contingencies can lead to deviations from expected functional responses to climate change as well as local variability in those responses. Our results form a set of interrelated hypotheses regarding soil microbial responses to climate change that warrant future empirical attention.     

人工电活性微生物菌群的设计与应用

包括产电菌群和噬电菌群的人工电活性微生物菌群(synthetic electroactive microbial consortia)通过菌种间的物质能量级联反应介导化学能与(光)电能间的相互转化，其可利用底物来源广泛、双向电子传递速率快、环境稳定性强，在清洁电能开发、废水处理、环境修复、生物固碳固氮以及生物燃料、无机纳米材料、高聚物等高值化学品合成等多个领域具有广泛的应用前景。针对人工电活性微生物菌群设计、构建与应用，本文总结电活性微生物菌群界面电子传递和种间电子传递机制，概括基于“劳力分工”原理设计构建人工电活性微生物菌群物质能量级联反应基本架构，总结菌群关系与菌群生态位优化等人工电活性微生物菌群工程化策略，分类列举人工电活性微生物菌群在利用廉价生物质产电、生物光伏固碳产电，光驱噬电生物菌群固氮等相关应用。最后对人工电活性微生物菌群未来研究方向进行了展望。     

A mini-review of microbial consortia: Their roles in aquatic production and biogeochemical cycling

Molecular oxygen (O₂) is a potent inhibitor of key microbial processes, including photosynthesis, N₂ fixation, denitrification, sulfate reduction, methanogenesis, iron, and metal reduction reactions. Prokaryote survival and proliferation in aquatic environments is often controlled by the ability to tolerate exposure to oxic conditions. Many prokaryotes do not have subcellular organelles for isolating O₂-producing from O₂-consuming processes and have developed consortial associations with other prokaryotes and eukaryotes that alleviate metabolic constraints of high O₂. Nutrient transformations often rely on appropriate cellular and microenvironmental, or microzonal, redox conditions. The spatial and temporal requirements for microenvironmental overlap among microbial groups involved in nutrient transformations necessitates close proximity and diffusional exchange with other biogeochemically distinct, yet complementary, microbial groups. Microbial consortia exist at different levels of community and metabolic complexity, as shown for detrital, microbial mat, biofilm, and planktonic microalgal-bacterial assemblages. To assess the macroscale impacts of consortial interactions, studies should focus on the range of relevant temporal (minutes to hours) and spatial (microns to centimeters) scales controlling microbial production, nutrient exchange, and cycling. In this review, we discuss the utility and application of techniques suitable for determining microscale consortial activity, production, community composition, and interactions in the context of larger scale aquatic ecosystem structure and function. Correspondence to: Hans W. Paerl.     

Earthworm invasions of ecosystems devoid of earthworms: effects on soil microbes

Recent studies document North American earthworm invasions and their profound effects on the structure of the soil profile, which is the habitat for soil microorganisms (mainly fungi and bacteria). Dramatic alterations made to these layers during earthworm invasion significantly change microbial community structure and therefore microbial activities such as C transformations. Understanding the impacts of earthworm invasion on the microbes themselves will give insight into earthworm effects on microbial activities. Bacterial and actinomycete communities in earthworm guts and casts have not been studied in environments recently invaded by earthworms. Earthworm invasion tended to decrease fungal species density and fungal species diversity and richness. The presence of earthworms decreased zygomycete species abundance probably due to disruption of fungal hyphae. Physical disruption of hyphae may also explain decreased mycorrhizal colonization rates, decreased mycorrhizal abundance and altered mycorrhizal morphology in the presence of earthworms. Mixing of organic layers into mineral soil during earthworm invasion tended to decrease microbial biomass in forest floor materials while increasing it in mineral soil. In newly invaded forest soils, microbial respiration and the metabolic quotient tended to decline. In forests where either the microbial community has had time to adapt to earthworm activities, or where the destruction of the forest floor is complete, as in invasions by the Asian Amynthas hawayanus, the presence of earthworms tends to increase the metabolic quotient indicating a shift to a smaller, more active microbial community.     

土壤微生物生物量碳氮磷与土壤酶化学计量对气候变化的响应机制

微生物和土壤酶是陆地生态系统中生物地球化学循环的重要驱动力,深入理解微生物在生态系统中的调节作用以及气候变化过程中微生物量和土壤酶的响应机制是生态学领域关注的重要科学问题.本研究从气候因素角度出发,基于生态化学计量学理论,综述了微生物和土壤酶在陆地生态系统碳氮磷循环中的作用,以及土壤微生物生物量碳氮磷和土壤酶化学计量对气候变化的响应机制,即: 改变微生物代谢速率和酶活性;调整微生物群落结构;调整微生物生物量碳氮磷与土壤酶化学计量特征;改变碳氮磷养分元素利用效率.最后分析当前研究的不足,并提出了该领域亟待解决的科学问题: 综合阐明土壤微生物和土壤酶对气候变化的响应机制;探究土壤微生物和胞外酶养分耦合机理;深入探究土壤微生物量和土壤酶化学计量特征对气候变化的适应对策.     

Metaproteomics: studying functional gene expression in microbial ecosystems

The recent availability of extensive metagenomic sequences from various environmental microbial communities has extended the postgenomic era to the field of environmental microbiology. Although still restricted to a small number of studies, metaproteomic investigations have revealed interesting aspects of functional gene expression within microbial habitats that contain limited microbial diversity. These studies highlight the potential of proteomics for the study of microbial consortia. However, the application of proteomic investigations to complex microbial assemblages such as seawater and soil still presents considerable challenges. Nonetheless, metaproteomics will enhance the understanding of the microbial world and link microbial community composition to function.     

Big questions, small worlds: microbial model systems in ecology

Although many biologists have embraced microbial model systems as tools to address genetic and physiological questions, the explicit use of microbial communities as model systems in ecology has traditionally been more restricted. Here, we highlight recent studies that use laboratory-based microbial model systems to address ecological questions. Such studies have significantly advanced our understanding of processes that have proven difficult to study in field systems, including the genetic and biochemical underpinnings of traits involved in ecological interactions, and the ecological differences driving evolutionary change. It is the simplicity of microbial model systems that makes them such powerful tools for the study of ecology. Such simplicity enables the high degrees of experimental control and replication that are necessary to address many questions that are inaccessible through field observation or experimentation.     

大兴安岭北部多年冻土区河岸森林湿地土壤性质和微生物呼吸活性特征

多年冻土区河岸森林湿地是水文、生态和生物化学过程的关键区域。本研究以河岸森林湿地及其与泥炭地的交错带土壤为对象,分析了腐殖质层和不同深度土壤理化性质、生态化学计量和微生物呼吸活性( 微生物生物量碳、基础呼吸、微生物熵和代谢熵)特征。结果表明: 与大兴安岭多年冻土区泥炭地和河岸森林湿地的交错带相比,河岸森林湿地土壤理化性质主要分异在20 cm土层以下,其总碳、总氮含量和碳磷比、氮磷比显著降低,生态化学计量特征的变化主要是由于氮含量变化引起的,说明河岸森林湿地土壤氮转移相对较快,存在氮限制;交错带湿地土壤中钠、镁、钾和钙含量主要在30 cm土层发生分异,而河岸森林湿地土壤中钠、镁、钾和钙含量主要在20 cm土层发生分异,其镁含量与土壤总碳、总氮和总磷含量显著相关,说明土壤镁含量是大兴安岭河岸森林湿地的重要营养元素;河岸森林湿地和交错带腐殖质层微生物呼吸活性高于其他层土壤,说明其易分解的碳组分含量高;河岸森林湿地和交错带土壤微生物呼吸活性与土壤理化性质、生态化学计量特征及营养元素的相关性存在差异,而河岸森林湿地土壤总氮含量与微生物呼吸活性显著相关,说明大兴安岭河岸带湿地土壤微生物活性受氮的限制。     

喀斯特峰丛洼地土壤剖面微生物特性对植被和坡位的响应

选取广西环江县喀斯特峰丛洼地:草丛(T)、灌丛(S)、原生林(PF)(中坡位)不同植被类型,原生林上、中、下不同坡位,按土壤发生层采集淋溶层(A层,0-10 cm)、过渡层(AB层,20-30 cm,草丛和灌丛;30-50 cm,原生林)、淀积层(B层,70-100cm)样品,研究土壤微生物量碳、氮(Soil microbial biomass carbon (SMBC)、soil microbial biomass nitrogen (SMBN))、微生物碳熵、氮熵(ratio of SMBC to soil organic carbon (qMBC)、ratio of SMBN to soil total nitrogen (qMBN))、土壤基础呼吸(soil basic respiration (SBR))以及代谢熵(microbial metabolic quotient(qCO2))的剖面分异特征及其影响因素.结果表明,植被、土层深度显著影响土壤微生物量及基础呼吸,随植被恢复,SMBC、SMBN、SBR由草丛、灌丛、原生林依次上升,并随土壤发生层位的加深逐渐减少,qCO2在3种植被类型间差异显著:T＞PF＞S;原生林A层SMBC,SMBN在各坡位间均显著高于AB层、B层,SBR在A层由下坡位至上坡位递减,而在AB和B层的上、下坡位间无显著差异,qCO2坡位间无显著差异(P＞0.05);SMBC与SMBN之间存在显著正相关(r=0.825,P＜0.01,n=45),且SMBC、SMBN、SBR分别与有机碳、全氮、碱解氮均呈显著正相关.因此,随植被恢复,土壤质量明显改善,且坡位对A层土壤的影响较AB层和B层更显著,对于维持土壤微生物调节的土壤养分循环功能,调控土壤氮素营养与土壤有机质同等重要,这为合理制订喀斯特生态恢复措施提供了理论依据.     

天台山七子花群落下土壤微生物生物量的季节动态

研究天台山七子花群落下土壤微生物生物量的季节变化规律及生态特性。根据实测数据分别对根际、根围微生物生物量碳、氮与土壤环境因子之间进行相关性分析,并建立了土壤微生物指标与环境因素之间的回归方程,以此为基础对天台山七子花群落下土壤微生物生物量的季节变化进行预测。回归分析表明：土壤温度、水分对微生物生物量的影响大于土壤pH值对微生物生物量的影响,而且土壤温度、水分对微生物生物量氮的影响大于对微生物生物量碳的影响。土壤温度对微生物生物量碳、氮的影响最大。     

不同森林恢复类型对土壤微生物群落的影响

为了评价不同森林恢复类型与方式对南方红壤丘陵区退化生态系统土壤微生物群落的影响,借助氯仿熏蒸法、平板涂抹法和BIOLOG检测法,比较研究了4种森林恢复类型土壤微生物的群落特征．结果表明,4种森林恢复类型土壤微生物生物量碳、细菌数量差异显著,2项指标均以天然次生林土壤最高,人工林次之,荒地最差;碳源平均颜色变化率(AWCD法)和微生物代谢多样性指数(丰富度和多样性)在5种植被类型的土壤中也有明显差异,其趋势与微生物量碳、细菌数量基本相同;天然次生林土壤微生物群落利用碳源的整体能力和功能多样性比人工林和荒地强．相关分析表明,0～20和20～40cm土壤微生物的代谢多样性与根系生物量紧密相关(r=0．933,P<0．05;r=0．925,P<0．05)．自然恢复更有利于改善土壤微生物的结构和功能．     

Deciphering microbial interactions in synthetic human gut microbiome communities

The ecological forces that govern the assembly and stability of the human gut microbiota remain unresolved. We developed a generalizable model‐guided framework to predict higher‐dimensional consortia from time‐resolved measurements of lower‐order assemblages. This method was employed to decipher microbial interactions in a diverse human gut microbiome synthetic community. We show that pairwise interactions are major drivers of multi‐species community dynamics, as opposed to higher‐order interactions. The inferred ecological network exhibits a high proportion of negative and frequent positive interactions. Ecological drivers and responsive recipient species were discovered in the network. Our model demonstrated that a prevalent positive and negative interaction topology enables robust coexistence by implementing a negative feedback loop that balances disparities in monospecies fitness levels. We show that negative interactions could generate history‐dependent responses of initial species proportions that frequently do not originate from bistability. Measurements of extracellular metabolites illuminated the metabolic capabilities of monospecies and potential molecular basis of microbial interactions. In sum, these methods defined the ecological roles of major human‐associated intestinal species and illuminated design principles of microbial communities.     

Roles of microorganisms other than Clostridium and Enterobacter in anaerobic fermentative biohydrogen production systems--a review

Anaerobic fermentative biohydrogen production, the conversion of organic substances especially from organic wastes to hydrogen gas, has become a viable and promising means of producing sustainable energy. Successful biological hydrogen production depends on the overall performance (results of interactions) of bacterial communities, i.e., mixed cultures in reactors. Mixed cultures might provide useful combinations of metabolic pathways for the processing of complex waste material ingredients, thereby supporting the more efficient decomposition and hydrogenation of biomass than pure bacteria species would. Therefore, understanding the relationships between variations in microbial composition and hydrogen production efficiency is the first step in constructing more efficient hydrogen-producing consortia, especially when complex and non-sterilized organic wastes are used as feeding substrates. In this review, we describe recent discoveries on bacterial community composition obtained from dark fermentation biohydrogen production systems, with emphasis on the possible roles of microorganisms that co-exist with common hydrogen producers.     

Effect of topsoil storage on microbial activity,primary production and decomposition potential

Summary The effects of disturbing (cultivating) and stockpiling prairie grassland topsoil on microbial activity, microbial biomass C, plant production and decomposition potentials were studied by measuring CO₂ efflux from unamended and glucose amended soil in the laboratory and by conducting a pot and litter bag study in the greenhouse. Stockpiling appeared to have very little effect on soil respiratory activity, but did reduce the microbial biomass C levels. Throughout the 3 year study the microbial biomass C in the surface soil of the stockpile was less than that in the undisturbed soil, while the biomass C in soil at the bottom of the stockpile was at no time significantly different from that in the undisturbed soil. The reduction in microbial biomass C in the surface soil immediately after stockpiling was attributed to a decrease in the soil organic C levels caused by a slight dilution of the topsoil with subsurface mineral soil, and the exposure of the stockpile surface to extreme environmental conditions. Soils from all depths of the stockpile responded more slowly to the addition of glucose than soil from the undisturbed and cultivated treatments even when no differences in biomass were detected between the undisturbed and stockpiled soils. It is postulated that the rapidity with which the soil microbial biomass responds to glucose additions may be a sensitive indicator of stress on the soil biological components. The reduction in biomass after storage for 1 year had no adverse effects on the decomposition or primary production potential of the stored soil. Rather, shoot production by fall rye was stimulated in the stored topsoil, presumably a result of better N nutrition.     

Synthetic Escherichia coli consortia engineered for syntrophy demonstrate enhanced biomass productivity

Synthetic Escherichia coli consortia engineered for syntrophy demonstrated enhanced biomass productivity relative to monocultures. Binary consortia were designed to mimic a ubiquitous, naturally occurring ecological template of primary productivity supported by secondary consumption. The synthetic consortia replicated this evolution-proven strategy by combining a glucose positive E. coli strain, which served as the system's primary producer, with a glucose negative E. coli strain which consumed metabolic byproducts from the primary producer. The engineered consortia utilized strategic division of labor to simultaneously optimize multiple tasks enhancing overall culture performance. Consortial interactions resulted in the emergent property of enhanced system biomass productivity which was demonstrated with three distinct culturing systems: batch, chemostat and biofilm growth. Glucose-based biomass productivity increased by ∼15, 20 and 50% compared to appropriate monoculture controls for these three culturing systems, respectively. Interestingly, the consortial interactions also produced biofilms with predictable, self-assembling, laminated microstructures. This study establishes a metabolic engineering paradigm which can be easily adapted to existing E. coli based bioprocesses to improve productivity based on a robust ecological theme.     

Evolution of soil organic matter changes using pyrolysis and metabolic indices: a comparison between organic and mineral fertilization

The aim of this study was to evaluate chemical and biochemical changes of organic matter in fertilized (ammonium nitrate) and amended (vermicompost and manure) soils using pyrolysis and metabolic indices. The metabolic potential [dehydrogenase (DH-ase)/water soluble organic carbon (WSOC)], the metabolic quotient (qCO2) and the microbial quotient (Cmic:Corg) were calculated as indices of soil organic matter evolution. Pyrolysis-gas chromatography (Py-GC) was used to study structural changes in the organic matter. Carbon forms and microbial biomass have been measured by dichromate oxidation and fumigation-extraction methods, respectively. Dehydrogenase activity has been tested using INT (p-Iodonitrotetrazolium violet) as substrate. The results showed that organic amendment increased soil microbial biomass and its activity which were strictly related to pyrolytic mineralization and humification indices (N/O, B/E3). Mineral fertilization caused a greater alteration of native soil organic matter than the organic amendments, in that a high release of WSOC and relatively large amounts of aliphatic pyrolytic products, were observed. Therefore, the pyrolysis and metabolic indices provided similar and complementary information on soil organic matter changes after mineral and organic fertilization.     

土壤微生物学特性对土壤健康的指示作用

土壤健康是陆地生态系统可持续发展的基础。作者通过概述土壤微生物学特性(土壤微生物群落结构、土壤微生物生物量、土壤酶活性)与土壤质量的关系, 阐明了土壤微生物对土壤健康的生物指示功能。研究表明: 土壤中细菌、真菌和放线菌的组成及其所占比率在一定程度上反映了土壤的肥力水平: 在土壤性质和肥水条件较好的土壤中, 细菌所占比率较高。土壤微生物生物量与土壤有机质含量密切相关, 而且土壤微生物生物量碳与土壤有机碳的比值(C_mic : C_org)和土壤微生物代谢熵(qCO2)的变化在一定程度上反映了土壤有机碳的利用效率。一般情况下, 土壤酶活性高的土壤中, 土壤微生物生物量碳、氮含量也高。因此, 土壤微生物学特性可以反映土壤质量的变化, 并可用作评价土壤健康的生物指标。     

生物质炭与氮肥配施对红壤线虫群落的影响

利用生物质炭改良土壤近年来受到关注,但仍缺乏对土壤动物群落变化的认识.基于野外定位试验,研究了不同用量的生物质炭(0、10、20、30、40 t·hm^-2)与氮肥(60、90、120 kg N·hm^-2)配施对干旱期和湿润期红壤理化性质和线虫群落的影响.结果表明： 施用生物质炭在干旱期和湿润期均显著影响土壤含水量和pH.随生物质炭施用量的增加,土壤含水量先增加后降低,而土壤pH保持增加的趋势.土壤微生物生物量碳氮、碳氮比及基础呼吸均受到生物质炭和氮肥的显著影响,且低量生物质炭对微生物生物量碳氮、碳氮比及基础呼吸有刺激作用,而高量生物质炭则对其有抑制作用.如生物质炭施用量低于30 t·hm^-2时,在干旱期和湿润期均促进土壤微生物活性.此外,生物质炭的效果也依赖于不同采样时期.如在施用量高于30 t·hm^-2时,微生物生物量碳在干旱期显著高于对照,在湿润期与对照无显著差异;而微生物生物量氮则呈相反趋势.可溶性有机物和矿质氮在干旱期受到生物质炭和氮肥的显著影响,但是在湿润期仅受到氮肥的影响.生物质炭、氮肥及二者的交互作用在干旱期和湿润期均显著影响线虫数量及营养类群的结构.高量生物质炭和氮肥配施能够提高土壤线虫的数量.值得注意的是,生物质炭显著提高了干旱期食真菌线虫的比例,尤其在干旱期趋势明显,暗示在生物质炭作用下土壤食物网结构趋向于以真菌主导的能流通道.总之,生物质炭对红壤的效果呈现出复杂的影响趋势,不仅依赖于生物质炭的施用量及与氮肥的交互作用,而且与红壤的采样时期有关,表明今后生物质炭的研究应结合多种生态因子.     

桂西南岩溶山地不同土地利用方式土壤微生物量及其活性特征

以广西平果县石漠化典型岩溶山地为研究区域,选择海拔接近的稀疏次生林地、灌丛、荒草地、裸地和农田等5种主要土地利用方式为研究对象,研究土壤微生物生物量及其活性的变异特征。结果表明:在不同土地利用方式下,随着植被的恢复,土壤养分含量不断提高,大小顺序表现为次生林>灌丛>农田>荒草地>裸地。土壤微生物量和呼吸强度变化显著(P<0.05),其中微生物量总体呈上升趋势,次生林和灌丛增幅较大,荒草地和裸地增幅较小;土壤基础呼吸强度除荒草地之外均显著增加,和土壤养分含量的变化趋势相一致。代谢熵(qCO2)变化规律不同,大小关系表现为:灌丛>农田>次生林>荒草地>裸地。不同土地利用方式下,由于相应地上、地下资源输入等环境因素的改变导致了土壤微生物量的差异性。为实现桂西南石漠化地区岩溶山地土壤生态系统的健康发展,从土壤生物学角度出发,积极推进植被生态恢复工程,尽可能减少人为活动对土地的干扰程度更有利于提高土壤质量。